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Sample records for conifer genomics resource

  1. Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource

    PubMed Central

    2013-01-01

    Background EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change. Results We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified. Conclusions We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and

  2. A white spruce gene catalog for conifer genome analyses.

    PubMed

    Rigault, Philippe; Boyle, Brian; Lepage, Pierre; Cooke, Janice E K; Bousquet, Jean; MacKay, John J

    2011-09-01

    Several angiosperm plant genomes, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), and grapevine (Vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. A gene catalog was developed for the conifer tree Picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cDNA sequencing to facilitate genome characterizations, comparative genomics, and gene mapping. The resource incorporates new and publicly available sequences into 27,720 cDNA clusters, 23,589 of which are represented by full-length insert cDNAs. Expressed sequence tags, mate-pair cDNA clone analysis, and custom sequencing were integrated through an iterative process to improve the accuracy of clustering outcomes. The entire catalog spans 30 Mb of unique transcribed sequence. We estimated that the P. glauca nuclear genome contains up to 32,520 transcribed genes owing to incomplete, partially sequenced, and unsampled transcripts and that its transcriptome could span up to 47 Mb. These estimates are in the same range as the Arabidopsis and rice transcriptomes. Next-generation methods confirmed and enhanced the catalog by providing deeper coverage for rare transcripts, by extending many incomplete clusters, and by augmenting the overall transcriptome coverage to 38 Mb of unique sequence. Genomic sample sequencing at 8.5% of the 19.8-Gb P. glauca genome identified 1,495 clusters representing highly repeated sequences among the cDNA clusters. With a conifer transcriptome in full view, functional and protein domain annotations clearly highlighted the divergences between conifers and angiosperms, likely reflecting their respective evolutionary paths.

  3. The Norway spruce genome sequence and conifer genome evolution.

    PubMed

    Nystedt, Björn; Street, Nathaniel R; Wetterbom, Anna; Zuccolo, Andrea; Lin, Yao-Cheng; Scofield, Douglas G; Vezzi, Francesco; Delhomme, Nicolas; Giacomello, Stefania; Alexeyenko, Andrey; Vicedomini, Riccardo; Sahlin, Kristoffer; Sherwood, Ellen; Elfstrand, Malin; Gramzow, Lydia; Holmberg, Kristina; Hällman, Jimmie; Keech, Olivier; Klasson, Lisa; Koriabine, Maxim; Kucukoglu, Melis; Käller, Max; Luthman, Johannes; Lysholm, Fredrik; Niittylä, Totte; Olson, Ake; Rilakovic, Nemanja; Ritland, Carol; Rosselló, Josep A; Sena, Juliana; Svensson, Thomas; Talavera-López, Carlos; Theißen, Günter; Tuominen, Hannele; Vanneste, Kevin; Wu, Zhi-Qiang; Zhang, Bo; Zerbe, Philipp; Arvestad, Lars; Bhalerao, Rishikesh; Bohlmann, Joerg; Bousquet, Jean; Garcia Gil, Rosario; Hvidsten, Torgeir R; de Jong, Pieter; MacKay, John; Morgante, Michele; Ritland, Kermit; Sundberg, Björn; Thompson, Stacey Lee; Van de Peer, Yves; Andersson, Björn; Nilsson, Ove; Ingvarsson, Pär K; Lundeberg, Joakim; Jansson, Stefan

    2013-05-30

    Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

  4. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)

    PubMed Central

    Ralph, Steven G; Chun, Hye Jung E; Kolosova, Natalia; Cooper, Dawn; Oddy, Claire; Ritland, Carol E; Kirkpatrick, Robert; Moore, Richard; Barber, Sarah; Holt, Robert A; Jones, Steven JM; Marra, Marco A; Douglas, Carl J; Ritland, Kermit; Bohlmann, Jörg

    2008-01-01

    Background Members of the pine family (Pinaceae), especially species of spruce (Picea spp.) and pine (Pinus spp.), dominate many of the world's temperate and boreal forests. These conifer forests are of critical importance for global ecosystem stability and biodiversity. They also provide the majority of the world's wood and fiber supply and serve as a renewable resource for other industrial biomaterials. In contrast to angiosperms, functional and comparative genomics research on conifers, or other gymnosperms, is limited by the lack of a relevant reference genome sequence. Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome annotation. Results As part of a conifer genomics program to characterize defense against insects and adaptation to local environments, and to discover genes for the production of biomaterials, we developed 20 standard, normalized or full-length enriched cDNA libraries from Sitka spruce (P. sitchensis), white spruce (P. glauca), and interior spruce (P. glauca-engelmannii complex). We sequenced and analyzed 206,875 3'- or 5'-end ESTs from these libraries, and developed a resource of 6,464 high-quality sequence-finished FLcDNAs from Sitka spruce. Clustering and assembly of 147,146 3'-end ESTs resulted in 19,941 contigs and 26,804 singletons, representing 46,745 putative unique transcripts (PUTs). The 6,464 FLcDNAs were all obtained from a single Sitka spruce genotype and represent 5,718 PUTs. Conclusion This paper provides detailed annotation and quality assessment of a large EST and FLcDNA resource for spruce. The 6,464 Sitka spruce FLcDNAs represent the third largest sequence-verified FLcDNA resource for any plant species, behind only rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), and the only substantial FLcDNA resource for a gymnosperm. Our emphasis on capturing FLcDNAs and ESTs from c

  5. Early genome duplications in conifers and other seed plants

    PubMed Central

    Li, Zheng; Baniaga, Anthony E.; Sessa, Emily B.; Scascitelli, Moira; Graham, Sean W.; Rieseberg, Loren H.; Barker, Michael S.

    2015-01-01

    Polyploidy is a common mode of speciation and evolution in angiosperms (flowering plants). In contrast, there is little evidence to date that whole genome duplication (WGD) has played a significant role in the evolution of their putative extant sister lineage, the gymnosperms. Recent analyses of the spruce genome, the first published conifer genome, failed to detect evidence of WGDs in gene age distributions and attributed many aspects of conifer biology to a lack of WGDs. We present evidence for three ancient genome duplications during the evolution of gymnosperms, based on phylogenomic analyses of transcriptomes from 24 gymnosperms and 3 outgroups. We use a new algorithm to place these WGD events in phylogenetic context: two in the ancestry of major conifer clades (Pinaceae and cupressophyte conifers) and one in Welwitschia (Gnetales). We also confirm that a WGD hypothesized to be restricted to seed plants is indeed not shared with ferns and relatives (monilophytes), a result that was unclear in earlier studies. Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms. As in the flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity. PMID:26702445

  6. Resource physiology of conifers: Acquisition, allocation, and utilization

    SciTech Connect

    Smith, W.K.; Hinckley, T.M.

    1995-03-01

    This book focuses on a synthetic view of the resource physiology of conifer trees with an emphasis on developing a perspective that can integrate across the biological hierarchy. This objective is in concert with more scientific goals of maintaining biological diversity and the sustainability of forest systems. The preservation of coniferous forest ecosystems is a major concern today. This volume deals with the topics of resource acquisition, allocation, and utilization in conifers. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

  7. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

    PubMed

    Warren, René L; Keeling, Christopher I; Yuen, Macaire Man Saint; Raymond, Anthony; Taylor, Greg A; Vandervalk, Benjamin P; Mohamadi, Hamid; Paulino, Daniel; Chiu, Readman; Jackman, Shaun D; Robertson, Gordon; Yang, Chen; Boyle, Brian; Hoffmann, Margarete; Weigel, Detlef; Nelson, David R; Ritland, Carol; Isabel, Nathalie; Jaquish, Barry; Yanchuk, Alvin; Bousquet, Jean; Jones, Steven J M; MacKay, John; Birol, Inanc; Bohlmann, Joerg

    2015-07-01

    White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation. PMID:26017574

  8. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

    PubMed

    Warren, René L; Keeling, Christopher I; Yuen, Macaire Man Saint; Raymond, Anthony; Taylor, Greg A; Vandervalk, Benjamin P; Mohamadi, Hamid; Paulino, Daniel; Chiu, Readman; Jackman, Shaun D; Robertson, Gordon; Yang, Chen; Boyle, Brian; Hoffmann, Margarete; Weigel, Detlef; Nelson, David R; Ritland, Carol; Isabel, Nathalie; Jaquish, Barry; Yanchuk, Alvin; Bousquet, Jean; Jones, Steven J M; MacKay, John; Birol, Inanc; Bohlmann, Joerg

    2015-07-01

    White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

  9. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function.

    PubMed

    Prunier, Julien; Verta, Jukka-Pekka; MacKay, John J

    2016-01-01

    Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.

  10. A White Spruce Gene Catalog for Conifer Genome Analyses1[W][OA

    PubMed Central

    Rigault, Philippe; Boyle, Brian; Lepage, Pierre; Cooke, Janice E.K.; Bousquet, Jean; MacKay, John J.

    2011-01-01

    Several angiosperm plant genomes, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), and grapevine (Vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. A gene catalog was developed for the conifer tree Picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cDNA sequencing to facilitate genome characterizations, comparative genomics, and gene mapping. The resource incorporates new and publicly available sequences into 27,720 cDNA clusters, 23,589 of which are represented by full-length insert cDNAs. Expressed sequence tags, mate-pair cDNA clone analysis, and custom sequencing were integrated through an iterative process to improve the accuracy of clustering outcomes. The entire catalog spans 30 Mb of unique transcribed sequence. We estimated that the P. glauca nuclear genome contains up to 32,520 transcribed genes owing to incomplete, partially sequenced, and unsampled transcripts and that its transcriptome could span up to 47 Mb. These estimates are in the same range as the Arabidopsis and rice transcriptomes. Next-generation methods confirmed and enhanced the catalog by providing deeper coverage for rare transcripts, by extending many incomplete clusters, and by augmenting the overall transcriptome coverage to 38 Mb of unique sequence. Genomic sample sequencing at 8.5% of the 19.8-Gb P. glauca genome identified 1,495 clusters representing highly repeated sequences among the cDNA clusters. With a conifer transcriptome in full view, functional and protein domain annotations clearly highlighted the divergences between conifers and angiosperms, likely reflecting their respective evolutionary paths. PMID:21730200

  11. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology.

    PubMed

    Uddenberg, Daniel; Akhter, Shirin; Ramachandran, Prashanth; Sundström, Jens F; Carlsbecker, Annelie

    2015-01-01

    Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right. PMID:26579190

  12. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology

    PubMed Central

    Uddenberg, Daniel; Akhter, Shirin; Ramachandran, Prashanth; Sundström, Jens F.; Carlsbecker, Annelie

    2015-01-01

    Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right. PMID:26579190

  13. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology.

    PubMed

    Uddenberg, Daniel; Akhter, Shirin; Ramachandran, Prashanth; Sundström, Jens F; Carlsbecker, Annelie

    2015-01-01

    Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.

  14. NCBI viral genomes resource.

    PubMed

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

  15. Ensembl comparative genomics resources

    PubMed Central

    Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J.; Searle, Stephen M. J.; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

  16. Ensembl comparative genomics resources.

    PubMed

    Herrero, Javier; Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J; Searle, Stephen M J; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.

  17. The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae

    PubMed Central

    Zheng, Renhua; Xu, Haibin; Zhou, Yanwei; Li, Meiping; Lu, Fengjuan; Dong, Yini; Liu, Xin; Chen, Jinhui; Shi, Jisen

    2016-01-01

    Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild. PMID:27560965

  18. The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae.

    PubMed

    Hao, Zhaodong; Cheng, Tielong; Zheng, Renhua; Xu, Haibin; Zhou, Yanwei; Li, Meiping; Lu, Fengjuan; Dong, Yini; Liu, Xin; Chen, Jinhui; Shi, Jisen

    2016-01-01

    Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild. PMID:27560965

  19. WheatGenome.info: A Resource for Wheat Genomics Resource.

    PubMed

    Lai, Kaitao

    2016-01-01

    An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

  20. WheatGenome.info: A Resource for Wheat Genomics Resource.

    PubMed

    Lai, Kaitao

    2016-01-01

    An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ . PMID:26519407

  1. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

    PubMed Central

    2012-01-01

    Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. Results To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Conclusions Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants. PMID:23102090

  2. Genomic Resources for Cancer Epidemiology

    Cancer.gov

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  3. Fungal genome resources at NCBI

    PubMed Central

    Robbertse, B.; Tatusova, T.

    2011-01-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools. PMID:22737589

  4. Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.

    PubMed

    Scott, Alison Dawn; Stenz, Noah W M; Ingvarsson, Pär K; Baum, David A

    2016-07-01

    Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade.

  5. Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.

    PubMed

    Scott, Alison Dawn; Stenz, Noah W M; Ingvarsson, Pär K; Baum, David A

    2016-07-01

    Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade. PMID:26996245

  6. MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants

    PubMed Central

    Gramzow, Lydia; Weilandt, Lisa; Theißen, Günter

    2014-01-01

    Background and Aims MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. Methods The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. Key Results Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11–14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14–16 Type II MADS-box genes. Conclusions The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS

  7. Gramene: a growing plant comparative genomics resource

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gramene (www.gramene.org) is a curated genetic, genomic and comparative genome analysis resource for the major crop species, such as rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project, with all data and software freely downloadable through the ftp site ...

  8. Gramene 2013: Comparative plant genomics resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework fo...

  9. Resources | Office of Cancer Genomics

    Cancer.gov

    OCG provides a variety of scientific and educational resources for both cancer researchers and members of the general public. These resources are divided into the following types: OCG-Supported Resources: Tools, databases, and reagents generated by initiated and completed OCG programs for researchers, educators, and students. (Note: Databases for current OCG programs are available through program-specific data matrices)

  10. Genomics and Bioinformatics Resources for Crop Improvement

    PubMed Central

    Mochida, Keiichi; Shinozaki, Kazuo

    2010-01-01

    Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology. PMID:20208064

  11. Genome-scale resources for Thermoanaerobacterium saccharolyticum

    DOE PAGESBeta

    Currie, Devin H.; Raman, Babu; Gowen, Christopher M.; Tschaplinski, Timothy J.; Land, Miriam L.; Brown, Steven D.; Covalla, Sean; Klingeman, Dawn Marie; Yang, Zamin Koo; Engle, Nancy L.; et al

    2015-06-26

    Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. For this research, a major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation.

  12. Developing genomic resources for the apiaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Apiaceae family includes carrot, celery, cilantro, dill, fennel and numerous other spice and medicinal crops. Carrot is the most economically important member of the Apiaceae with an annual value of $600 M in the United States alone. There are few genomic resources for carrot or other Apiaceae, ...

  13. Sequence resources at the Candida Genome Database.

    PubMed

    Arnaud, Martha B; Costanzo, Maria C; Skrzypek, Marek S; Shah, Prachi; Binkley, Gail; Lane, Christopher; Miyasato, Stuart R; Sherlock, Gavin

    2007-01-01

    The Candida Genome Database (CGD, http://www.candidagenome.org/) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic pathogen Candida albicans. With the recent release of a new assembly of the C.albicans genome, Assembly 20, C.albicans genomics has entered a new era. Although the C.albicans genome assembly continues to undergo refinement, multiple assemblies and gene nomenclatures will remain in widespread use by the research community. CGD has now taken on the responsibility of maintaining the most up-to-date version of the genome sequence by providing the data from this new assembly alongside the data from the previous assemblies, as well as any future corrections and refinements. In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD provides. CGD is freely accessible at http://www.candidagenome.org/ and CGD curators may be contacted by email at candida-curator@genome.stanford.edu.

  14. Saccharomyces Genome Database: the genomics resource of budding yeast

    PubMed Central

    Cherry, J. Michael; Hong, Eurie L.; Amundsen, Craig; Balakrishnan, Rama; Binkley, Gail; Chan, Esther T.; Christie, Karen R.; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Karra, Kalpana; Krieger, Cynthia J.; Miyasato, Stuart R.; Nash, Rob S.; Park, Julie; Skrzypek, Marek S.; Simison, Matt; Weng, Shuai; Wong, Edith D.

    2012-01-01

    The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use. PMID:22110037

  15. Saccharomyces Genome Database: the genomics resource of budding yeast.

    PubMed

    Cherry, J Michael; Hong, Eurie L; Amundsen, Craig; Balakrishnan, Rama; Binkley, Gail; Chan, Esther T; Christie, Karen R; Costanzo, Maria C; Dwight, Selina S; Engel, Stacia R; Fisk, Dianna G; Hirschman, Jodi E; Hitz, Benjamin C; Karra, Kalpana; Krieger, Cynthia J; Miyasato, Stuart R; Nash, Rob S; Park, Julie; Skrzypek, Marek S; Simison, Matt; Weng, Shuai; Wong, Edith D

    2012-01-01

    The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use. PMID:22110037

  16. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

    PubMed

    Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

    2013-02-01

    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

  17. Development of chloroplast genomic resources for Cynara.

    PubMed

    Curci, Pasquale L; De Paola, Domenico; Sonnante, Gabriella

    2016-03-01

    In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level. PMID:26354522

  18. Genomics data resources: frameworks and standards.

    PubMed

    Wilkinson, Mark D

    2012-01-01

    The emergence of genomics tools for the evolutionary and comparative biology community led to a rapid explosion in the number of online resources targeted at this specialized community, including Web-based comparative genomics software, such as the Artemis Comparison Tool (WebACT); databases, such as PaleoDB, Global Biodiversity Information Facility, and TreeBase; and knowledge frameworks, such as the Evolution Ontology. Unfortunately, these providers are largely independent of one another and therefore the individual resources do not share any centralized plan for how the data or tools would or should be provided. As a result, there are a myriad of often incompatible technologies and frameworks being used by this community of providers. In this chapter, we explore approaches to online resource publication, both those already in use by the community, as well as new and emergent frameworks and standards. Exploration of the strengths and weaknesses of each approach, together with a brief exploration of the philosophy or informatics theory behind the varying approaches, will hopefully help readers as they navigate this data space. The discussion is constructed such that it lays the groundwork for exploration of a new global standard for data and knowledge representation--"The Semantic Web"--that holds promise of providing solutions to many of the complexities users face in their attempts to discover and integrate biodiversity data, and examples are provided.

  19. MycoCosm, an Integrated Fungal Genomics Resource

    SciTech Connect

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  20. Intraspecific growth and functional leaf trait responses to natural soil resource gradients for conifer species with contrasting leaf habit.

    PubMed

    Walters, Michael B; Gerlach, John P

    2013-03-01

    Interspecific relationships among species mean leaf traits, performance and species resource/climate distributions help provide the foundation for a predictive, functionally based plant ecology. Intraspecific responses of leaf traits and performance to resource gradients and how these vary among species may be equally important but have received less attention. Here, we examine relationships between proxies of soil resource availability, leaf traits and growth (height at 25 years, SI25) for winter deciduous Larix decidua Mill. and evergreen Pinus resinosa Ait. trees distributed over soil resource gradients in the Great Lakes region of North America. We predicted that (i) leaf trait responses to soil resources within species will be similar to reported distributions of mean leaf traits over soil resource gradients among species; (ii) soil resource-related variation in leaf traits can help explain SI25; and (iii) SI25 will be greater for Larix than Pinus at higher soil resources and greater for Pinus than Larix at lower soil resources and this pattern will be associated with species differences in leaf trait responses to soil resources. Among the measured leaf traits (live N, Mg, Ca, K, P, and Mn, litter N, N resorption, carbon isotope discrimination, specific leaf area, lifespan), soil resources only impacted live and litter N for both species and K for Pinus. In turn, only the leaf traits responsive to soil resources affected SI25 in the expected manner. Larix had greater SI25 than Pinus across soil resource gradients and both species had similar growth and leaf trait sensitivities to resources. In summary: (i) several leaf traits reported to be associated with performance and edaphic distributions across species were, within species, unresponsive to nitrogen and water availability and unrelated to growth; (ii) leaf N showed high plasticity to soil resources and this plasticity was functionally relevant to growth over its entire range of response; (iii) large

  1. Update on RefSeq microbial genomes resources.

    PubMed

    Tatusova, Tatiana; Ciufo, Stacy; Federhen, Scott; Fedorov, Boris; McVeigh, Richard; O'Neill, Kathleen; Tolstoy, Igor; Zaslavsky, Leonid

    2015-01-01

    NCBI RefSeq genome collection http://www.ncbi.nlm.nih.gov/genome represents all three major domains of life: Eukarya, Bacteria and Archaea as well as Viruses. Prokaryotic genome sequences are the most rapidly growing part of the collection. During the year of 2014 more than 10,000 microbial genome assemblies have been publicly released bringing the total number of prokaryotic genomes close to 30,000. We continue to improve the quality and usability of the microbial genome resources by providing easy access to the data and the results of the pre-computed analysis, and improving analysis and visualization tools. A number of improvements have been incorporated into the Prokaryotic Genome Annotation Pipeline. Several new features have been added to RefSeq prokaryotic genomes data processing pipeline including the calculation of genome groups (clades) and the optimization of protein clusters generation using pan-genome approach.

  2. The Brachypodium genome sequence: a resource for oat genomics research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oat (Avena sativa) is an important cereal crop used as both an animal feed and for human consumption. Genetic and genomic research on oat is hindered because it is hexaploid and possesses a large (13 Gb) genome. Diploid Avena relatives have been employed for genetic and genomic studies, but only mod...

  3. The Anadara trapezia transcriptome: a resource for molluscan physiological genomics.

    PubMed

    Prentis, Peter J; Pavasovic, Ana

    2014-12-01

    In this study we undertook deep sequencing of the blood cockle, Anadara trapezia, transcriptome to generate genomic resources for future functional genomics analyses. Over 27 million high quality paired end reads were assembled into 75024 contigs. Of these contigs, 29013 (38.7%) received significant BLASTx hits and gene ontology (GO) terms were assigned to 13718 of these sequences. This resource will facilitate physiological genomic studies to test the gene expression response of A. trapezia to various environmental stresses. PMID:25151889

  4. Genomic resources in fruit plants: an assessment of current status.

    PubMed

    Rai, Manoj K; Shekhawat, N S

    2015-01-01

    The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.

  5. Sources for Comparative Studies of Placentation. II. Genomic Resources

    PubMed Central

    Wildman, Derek E.

    2008-01-01

    The genomes of dozens of placental mammal species are now publicly available. These genome sequences have the potential to provide insight into the development and evolution of the placenta. In particular, the variable anatomy of the placenta has likely been affected by natural selection on the genomes of living and extinct mammals. In this note the current availability of mammal genome sequences is reviewed, and strengths and limitations of these data are discussed. Additionally, museums, zoos, and commercial entities are available to provide genomic resources to the placental research community. Recommendations for tissue storage conditions of placentas in genomic research are given. PMID:18155141

  6. Gramene 2016: comparative plant genomics and pathway resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the data...

  7. Genome resource banking of biomedically important laboratory animals.

    PubMed

    Agca, Yuksel

    2012-11-01

    Genome resource banking is the systematic collection, storage, and redistribution of biomaterials in an organized, logistical, and secure manner. Genome cryobanks usually contain biomaterials and associated genomic information essential for progression of biomedicine, human health, and research. In that regard, appropriate genome cryobanks could provide essential biomaterials for both current and future research projects in the form of various cell types and tissues, including sperm, oocytes, embryos, embryonic or adult stem cells, induced pluripotent stem cells, and gonadal tissues. In addition to cryobanked germplasm, cryobanking of DNA, serum, blood products, and tissues from scientifically, economically, and ecologically important species has become a common practice. For revitalization of the whole organism, cryopreserved germplasm in conjunction with assisted reproductive technologies, offer a powerful approach for research model management, as well as assisting in animal production for agriculture, conservation, and human reproductive medicine. Recently, many developed and developing countries have allocated substantial resources to establish genome resources banks which are responsible for safeguarding scientifically, economically, and ecologically important wild type, mutant, and transgenic plants, fish, and local livestock breeds, as well as wildlife species. This review is dedicated to the memory of Dr. John K. Critser, who has made profound contributions to the science of cryobiology and establishment of genome research and resources centers for mice, rats, and swine. Emphasis will be given to application of genome resource banks to species with substantial contributions to the advancement of biomedicine and human health. PMID:22981880

  8. The KEGG resource for deciphering the genome.

    PubMed

    Kanehisa, Minoru; Goto, Susumu; Kawashima, Shuichi; Okuno, Yasushi; Hattori, Masahiro

    2004-01-01

    A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.

  9. The KEGG resource for deciphering the genome.

    PubMed

    Kanehisa, Minoru; Goto, Susumu; Kawashima, Shuichi; Okuno, Yasushi; Hattori, Masahiro

    2004-01-01

    A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database. PMID:14681412

  10. Genome Resource Banking of Biomedically Important Laboratory Animals

    PubMed Central

    Agca, Yuksel

    2014-01-01

    Genome resource banking (GRB) is the systematic collection, storage, and re-distribution of biomaterials in an organized, logistical, and secure manner. Genome cyrobanks usually contain biomaterials and associated genomic information essential for progression of biomedicine, human health, and research. In that regard, appropriate genome cryobanks could provide essential biomaterials for both current and future research projects in the form of various cell types and tissues, including sperm, oocytes, embryos, embryonic or adult stem cells, induced pluripotent stem cells, and gonadal tissues. In addition to cryobanked germplasm, cryobanking of DNA, serum, blood products, and tissues from scientifically, economically and ecologically important species has become a common practice. For revitalization of the whole organism, cryopreserved germplasm in conjunction with assisted reproductive technologies (ART), offer a powerful approach for research model management, as well as assisting in animal production for agriculture, conservation, and human reproductive medicine. Recently, many developed and developing countries have allocated substantial resources to establish genome resources banks which are responsible for safeguarding scientifically, economically and ecologically important wild type, mutant and transgenic plants, fish, and local livestock breeds, as well as wildlife species. This review is dedicated to the memory of Dr. John K. Critser, who had made profound contributions to the science of cryobiology and establishment of genome research and resources centers for mice, rats and swine. Emphasis will be given to application of GRBs to species with substantial contributions to the advancement of biomedicine and human health. PMID:22981880

  11. The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

    PubMed

    Hamilton, John P; Neeno-Eckwall, Eric C; Adhikari, Bishwo N; Perna, Nicole T; Tisserat, Ned; Leach, Jan E; Lévesque, C André; Buell, C Robin

    2011-01-01

    The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu.

  12. Resources for Biological Annotation of the Drosophila Genome

    SciTech Connect

    Gerald M. Rubin

    2005-08-08

    This project supported seed money for the development of cDNA and genetic resources to support studies of the Drosophila melanogaster genome. Key publications supported by this work that provide additional detail: (1) ''The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes''; and (2) ''The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes''.

  13. Gramene 2016: comparative plant genomics and pathway resources.

    PubMed

    Tello-Ruiz, Marcela K; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A; Huerta, Laura; Keays, Maria; Tang, Y Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J; Jaiswal, Pankaj; Ware, Doreen

    2016-01-01

    Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.

  14. Gramene 2016: comparative plant genomics and pathway resources

    PubMed Central

    Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

    2016-01-01

    Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

  15. Gramene 2016: comparative plant genomics and pathway resources.

    PubMed

    Tello-Ruiz, Marcela K; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A; Huerta, Laura; Keays, Maria; Tang, Y Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J; Jaiswal, Pankaj; Ware, Doreen

    2016-01-01

    Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

  16. Genomics and bioinformatics resources for translational science in Rosaceae.

    PubMed

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  17. PhytoPath: an integrative resource for plant pathogen genomics

    PubMed Central

    Pedro, Helder; Maheswari, Uma; Urban, Martin; Irvine, Alistair George; Cuzick, Alayne; McDowall, Mark D.; Staines, Daniel M.; Kulesha, Eugene; Hammond-Kosack, Kim Elizabeth; Kersey, Paul Julian

    2016-01-01

    PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species. PMID:26476449

  18. PhytoPath: an integrative resource for plant pathogen genomics.

    PubMed

    Pedro, Helder; Maheswari, Uma; Urban, Martin; Irvine, Alistair George; Cuzick, Alayne; McDowall, Mark D; Staines, Daniel M; Kulesha, Eugene; Hammond-Kosack, Kim Elizabeth; Kersey, Paul Julian

    2016-01-01

    PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species.

  19. Assembly: a resource for assembled genomes at NCBI

    PubMed Central

    Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

    2016-01-01

    The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

  20. Genome resource for the Indonesian coelacanth, Latimeria menadoensis.

    PubMed

    Danke, Joshua; Miyake, Tsutomu; Powers, Thomas; Schein, Jacqueline; Shin, Heesun; Bosdet, Ian; Erdmann, Mark; Caldwell, Roy; Amemiya, Chris T

    2004-03-01

    We have generated a BAC library from the Indonesian coelacanth, Latimeria menadoensis. This library was generated using genomic DNA of nuclei isolated from heart tissue, and has an average insert size of 171 kb. There are a total of 288 384-well microtiter dishes in the library (110,592 clones) and its genomic representation is estimated to encompass > or = 7X coverage based on the amount of DNA presumably cloned in the library as well as via hybridization with probes to a small set of single copy genes. This genomic resource has been made available to the public and should prove useful to the scientific community for many applications, including comparative genomics, molecular evolution and conservation genetics.

  1. Genomic resource development for shellfish of conservation concern.

    PubMed

    Timmins-Schiffman, Emma B; Friedman, Carolyn S; Metzger, Dave C; White, Samuel J; Roberts, Steven B

    2013-03-01

    Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species.

  2. Quantitative prediction of genome-wide resource allocation in bacteria.

    PubMed

    Goelzer, Anne; Muntel, Jan; Chubukov, Victor; Jules, Matthieu; Prestel, Eric; Nölker, Rolf; Mariadassou, Mahendra; Aymerich, Stéphane; Hecker, Michael; Noirot, Philippe; Becher, Dörte; Fromion, Vincent

    2015-11-01

    Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by simplifying hypotheses. Here, we show that the constraint-based modeling method Resource Balance Analysis (RBA), calibrated using genome-wide absolute protein quantification data, accurately predicts resource allocation in the model bacterium Bacillus subtilis for a wide range of growth conditions. The regulation of most cellular processes is consistent with the objective of growth rate maximization except for a few suboptimal processes which likely integrate more complex objectives such as coping with stressful conditions and survival. As a proof of principle by using simulations, we illustrated how calibrated RBA could aid rational design of strains for maximizing protein production, offering new opportunities to investigate design principles in prokaryotes and to exploit them for biotechnological applications.

  3. PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants[W

    PubMed Central

    Proost, Sebastian; Van Bel, Michiel; Sterck, Lieven; Billiau, Kenny; Van Parys, Thomas; Van de Peer, Yves; Vandepoele, Klaas

    2009-01-01

    The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage. PMID:20040540

  4. PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

    PubMed

    Proost, Sebastian; Van Bel, Michiel; Sterck, Lieven; Billiau, Kenny; Van Parys, Thomas; Van de Peer, Yves; Vandepoele, Klaas

    2009-12-01

    The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.

  5. Genomic resources for flatfish research and their applications.

    PubMed

    Cerdà, J; Douglas, S; Reith, M

    2010-10-01

    Flatfishes are a group of teleosts of high commercial and environmental interest, whose biology is still poorly understood. The recent rapid development of different 'omic' technologies is, however, enhancing the knowledge of the complex genetic control underlying different physiological processes of flatfishes. This review describes the different functional genomic approaches and resources currently available for flatfish research and summarizes different areas where microarray-based gene expression analysis has been applied. The increase in genome sequencing data has also allowed the construction of genetic linkage maps in different flatfish species; these maps are invaluable for investigating genome organization and identifying genetic traits of commercial interest. Despite the significant progress in this field, the genomic resources currently available for flatfish are still scarce. Further intensive research should be carried out to develop larger genomic sequence databases, high-density microarrays and, more detailed, complete linkage maps, using second-generation sequencing platforms. These tools will be crucial for further expanding the knowledge of flatfish physiology, and it is predicted that they will have important implications for wild fish population management, improved fish welfare and increased productivity in aquaculture.

  6. A public resource facilitating clinical use of genomes

    PubMed Central

    Ball, Madeleine P.; Thakuria, Joseph V.; Zaranek, Alexander Wait; Clegg, Tom; Rosenbaum, Abraham M.; Wu, Xiaodi; Angrist, Misha; Bhak, Jong; Bobe, Jason; Callow, Matthew J.; Cano, Carlos; Chou, Michael F.; Chung, Wendy K.; Douglas, Shawn M.; Estep, Preston W.; Gore, Athurva; Hulick, Peter; Labarga, Alberto; Lee, Je-Hyuk; Lunshof, Jeantine E.; Kim, Byung Chul; Kim, Jong-Il; Li, Zhe; Murray, Michael F.; Nilsen, Geoffrey B.; Peters, Brock A.; Raman, Anugraha M.; Rienhoff, Hugh Y.; Robasky, Kimberly; Wheeler, Matthew T.; Vandewege, Ward; Vorhaus, Daniel B.; Yang, Joyce L.; Yang, Luhan; Aach, John; Ashley, Euan A.; Drmanac, Radoje; Kim, Seong-Jin; Li, Jin Billy; Peshkin, Leonid; Seidman, Christine E.; Seo, Jeong-Sun; Zhang, Kun; Rehm, Heidi L.; Church, George M.

    2012-01-01

    Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved “open consent” process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain—we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research. PMID:22797899

  7. PlantGDB: a resource for comparative plant genomics

    PubMed Central

    Duvick, Jon; Fu, Ann; Muppirala, Usha; Sabharwal, Mukul; Wilkerson, Matthew D.; Lawrence, Carolyn J.; Lushbough, Carol; Brendel, Volker

    2008-01-01

    PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training. PMID:18063570

  8. Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics.

    PubMed

    Yue, Junyang; Liu, Jian; Ban, Rongjun; Tang, Wei; Deng, Lin; Fei, Zhangjun; Liu, Yongsheng

    2015-01-01

    The Kiwifruit Information Resource (KIR) is dedicated to maintain and integrate comprehensive datasets on genomics, functional genomics and transcriptomics of kiwifruit (Actinidiaceae). KIR serves as a central access point for existing/new genomic and genetic data. KIR also provides researchers with a variety of visualization and analysis tools. Current developments include the updated genome structure of Actinidia chinensis cv. Hongyang and its newest genome annotation, putative transcripts, gene expression, physical markers of genetic traits as well as relevant publications based on the latest genome assembly. Nine thousand five hundred and forty-seven new transcripts are detected and 21 132 old transcripts are changed. At the present release, the next-generation transcriptome sequencing data has been incorporated into gene models and splice variants. Protein-protein interactions are also identified based on experimentally determined orthologous interactions. Furthermore, the experimental results reported in peer-reviewed literature are manually extracted and integrated within a well-developed query page. In total, 122 identifications are currently associated, including commonly used gene names and symbols. All KIR datasets are helpful to facilitate a broad range of kiwifruit research topics and freely available to the research community. Database URL: http://bdg.hfut.edu.cn/kir/index.html. PMID:26656885

  9. Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics.

    PubMed

    Yue, Junyang; Liu, Jian; Ban, Rongjun; Tang, Wei; Deng, Lin; Fei, Zhangjun; Liu, Yongsheng

    2015-01-01

    The Kiwifruit Information Resource (KIR) is dedicated to maintain and integrate comprehensive datasets on genomics, functional genomics and transcriptomics of kiwifruit (Actinidiaceae). KIR serves as a central access point for existing/new genomic and genetic data. KIR also provides researchers with a variety of visualization and analysis tools. Current developments include the updated genome structure of Actinidia chinensis cv. Hongyang and its newest genome annotation, putative transcripts, gene expression, physical markers of genetic traits as well as relevant publications based on the latest genome assembly. Nine thousand five hundred and forty-seven new transcripts are detected and 21 132 old transcripts are changed. At the present release, the next-generation transcriptome sequencing data has been incorporated into gene models and splice variants. Protein-protein interactions are also identified based on experimentally determined orthologous interactions. Furthermore, the experimental results reported in peer-reviewed literature are manually extracted and integrated within a well-developed query page. In total, 122 identifications are currently associated, including commonly used gene names and symbols. All KIR datasets are helpful to facilitate a broad range of kiwifruit research topics and freely available to the research community. Database URL: http://bdg.hfut.edu.cn/kir/index.html.

  10. Resources for Functional Genomics Studies in Drosophila melanogaster

    PubMed Central

    Mohr, Stephanie E.; Hu, Yanhui; Kim, Kevin; Housden, Benjamin E.; Perrimon, Norbert

    2014-01-01

    Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, “meta” information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally. PMID:24653003

  11. Genomic resources in mungbean for future breeding programs

    PubMed Central

    Kim, Sue K.; Nair, Ramakrishnan M.; Lee, Jayern; Lee, Suk-Ha

    2015-01-01

    Among the legume family, mungbean (Vigna radiata) has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A) and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata) has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement. PMID:26322067

  12. MorusDB: a resource for mulberry genomics and genome biology.

    PubMed

    Li, Tian; Qi, Xiwu; Zeng, Qiwei; Xiang, Zhonghuai; He, Ningjia

    2014-01-01

    Mulberry is an important cultivated plant that has received the attention of biologists interested in sericulture and plant-insect interaction. Morus notabilis, a wild mulberry species with a minimal chromosome number is an ideal material for whole-genome sequencing and assembly. The genome and transcriptome of M. notabilis were sequenced and analyzed. In this article, a web-based and open-access database, the Morus Genome Database (MorusDB), was developed to enable easy-to-access and data mining. The MorusDB provides an integrated data source and an easy accession of mulberry large-scale genomic sequencing and assembly, predicted genes and functional annotations, expressed sequence tags (ESTs), transposable elements (TEs), Gene Ontology (GO) terms, horizontal gene transfers between mulberry and silkworm and ortholog and paralog groups. Transcriptome sequencing data for M. notabilis root, leaf, bark, winter bud and male flower can also be searched and downloaded. Furthermore, MorusDB provides an analytical workbench with some built-in tools and pipelines, such as BLAST, Search GO, Mulberry GO and Mulberry GBrowse, to facilitate genomic studies and comparative genomics. The MorusDB provides important genomic resources for scientists working with mulberry and other Moraceae species, which include many important fruit crops. Designed as a basic platform and accompanied by the SilkDB, MorusDB strives to be a comprehensive platform for the silkworm-mulberry interaction studies. Database URL: http://morus.swu.edu.cn/morusdb.

  13. Floral gene resources from basal angiosperms for comparative genomics research

    PubMed Central

    Albert, Victor A; Soltis, Douglas E; Carlson, John E; Farmerie, William G; Wall, P Kerr; Ilut, Daniel C; Solow, Teri M; Mueller, Lukas A; Landherr, Lena L; Hu, Yi; Buzgo, Matyas; Kim, Sangtae; Yoo, Mi-Jeong; Frohlich, Michael W; Perl-Treves, Rafael; Schlarbaum, Scott E; Bliss, Barbara J; Zhang, Xiaohong; Tanksley, Steven D; Oppenheimer, David G; Soltis, Pamela S; Ma, Hong; dePamphilis, Claude W; Leebens-Mack, James H

    2005-01-01

    Background The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. Results Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. Conclusion Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and

  14. Tetrahymena functional genomics database (TetraFGD): an integrated resource for Tetrahymena functional genomics.

    PubMed

    Xiong, Jie; Lu, Yuming; Feng, Jinmei; Yuan, Dongxia; Tian, Miao; Chang, Yue; Fu, Chengjie; Wang, Guangying; Zeng, Honghui; Miao, Wei

    2013-01-01

    The ciliated protozoan Tetrahymena thermophila is a useful unicellular model organism for studies of eukaryotic cellular and molecular biology. Researches on T. thermophila have contributed to a series of remarkable basic biological principles. After the macronuclear genome was sequenced, substantial progress has been made in functional genomics research on T. thermophila, including genome-wide microarray analysis of the T. thermophila life cycle, a T. thermophila gene network analysis based on the microarray data and transcriptome analysis by deep RNA sequencing. To meet the growing demands for the Tetrahymena research community, we integrated these data to provide a public access database: Tetrahymena functional genomics database (TetraFGD). TetraFGD contains three major resources, including the RNA-Seq transcriptome, microarray and gene networks. The RNA-Seq data define gene structures and transcriptome, with special emphasis on exon-intron boundaries; the microarray data describe gene expression of 20 time points during three major stages of the T. thermophila life cycle; the gene network data identify potential gene-gene interactions of 15 049 genes. The TetraFGD provides user-friendly search functions that assist researchers in accessing gene models, transcripts, gene expression data and gene-gene relationships. In conclusion, the TetraFGD is an important functional genomic resource for researchers who focus on the Tetrahymena or other ciliates. Database URL: http://tfgd.ihb.ac.cn/

  15. SGR: an online genomic resource for the woodland strawberry

    PubMed Central

    2013-01-01

    Background Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system and an emerging model for the Rosaceae family. An ancestral F. vesca genome contributed to the genome of the octoploid dessert strawberry (F. ×ananassa), and the extant genome exhibits synteny with other commercially important members of the Rosaceae family such as apple and peach. To provide a molecular description of floral organ and fruit development at the resolution of specific tissues and cell types, RNAs from flowers and early developmental stage fruit tissues of the inbred F. vesca line YW5AF7 were extracted and the resulting cDNA libraries sequenced using an Illumina HiSeq2000. To enable easy access as well as mining of this two-dimensional (stage and tissue) transcriptome dataset, a web-based database, the Strawberry Genomic Resource (SGR), was developed. Description SGR is a web accessible database that contains sample description, sample statistics, gene annotation, and gene expression analysis. This information can be accessed publicly from a web-based interface at http://bioinformatics.towson.edu/strawberry/Default.aspx. The SGR website provides user friendly search and browse capabilities for all the data stored in the database. Users are able to search for genes using a gene ID or description or obtain differentially expressed genes by entering different comparison parameters. Search results can be downloaded in a tabular format compatible with Microsoft excel application. Aligned reads to individual genes and exon/intron structures are displayed using the genome browser, facilitating gene re-annotation by individual users. Conclusions The SGR database was developed to facilitate dissemination and data mining of extensive floral and fruit transcriptome data in the woodland strawberry. It enables users to mine the data in different ways to study different pathways or biological processes during

  16. Genomic Resources Notes accepted 1 February 2015 - 31 March 2015.

    PubMed

    Arthofer, Wolfgang; Bertini, Laura; Caruso, Carla; Cicconardi, Francesco; Delph, Lynda F; Fields, Peter D; Ikeda, Minoru; Minegishi, Yuki; Proietti, Silvia; Ritthammer, Heike; Schlick-Steiner, Birgit C; Steiner, Florian M; Wachter, Gregor A; Wagner, Herbert C; Weingartner, Laura A

    2015-07-01

    This article documents the public availability of (i) raw transcriptome sequence data, assembled contigs and BLAST hits of the Antarctic plant Colobanthus quitensis grown in two different climatic conditions, (ii) the draft genome sequence data (raw reads, assembled contigs and unassembled reads) and RAD-tag read data of the marbled flounder Pseudopleuronectes yokohamae, (iii) transcriptome resources from four white campion (Silene latifolia) individuals from two morphologically divergent populations and (iv) nuclear DNA markers from 454 sequencing of reduced representation libraries (RRL) based on amplified fragment length polymorphism (AFLP) PCR products of four species of ants in the genus Tetramorium. PMID:26095006

  17. Learning about the Human Genome. Part 2: Resources for Science Educators. ERIC Digest.

    ERIC Educational Resources Information Center

    Haury, David L.

    This ERIC Digest identifies how the human genome project fits into the "National Science Education Standards" and lists Human Genome Project Web sites found on the World Wide Web. It is a resource companion to "Learning about the Human Genome. Part 1: Challenge to Science Educators" (Haury 2001). The Web resources and instructional materials can…

  18. More genomic resources for less-studied crops.

    PubMed

    Varshney, Rajeev K; Glaszmann, Jean-Christophe; Leung, Hei; Ribaut, Jean-Marcel

    2010-09-01

    Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and diversity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic diversity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries. PMID:20692061

  19. Development of peanut expessed sequence tag-based genomic resources and tools

    Technology Transfer Automated Retrieval System (TEKTRAN)

    U.S. Peanut Genome Initiative (PGI) has widely recognized the need for peanut genome tools and resources development for mitigating peanut allergens and food safety. Genomics such as Expressed Sequence Tag (EST), microarray technologies, and whole genome sequencing provides robotic tools for profili...

  20. Development of peanut EST (expressed sequence tag)-based genomic resources and tools

    Technology Transfer Automated Retrieval System (TEKTRAN)

    U.S. Peanut Genome Initiative (PGI) has widely recognized the need for peanut genome tools and resources development for mitigating peanut allergens and food safety. Genomics such as Expressed Sequence Tag (EST), microarray technologies, and whole genome sequencing provides robotic tools for profili...

  1. The Xenopus ORFeome: A resource that enables functional genomics

    PubMed Central

    Grant, Ian M.; Balcha, Dawit; Hao, Tong; Shen, Yun; Trivedi, Prasad; Patrushev, Ilya; Fortriede, Joshua D.; Karpinka, John B.; Liu, Limin; Zorn, Aaron M.; Stukenberg, P. Todd; Hill, David E.; Gilchrist, Michael J.

    2015-01-01

    Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5′ and 3′ end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling. PMID:26391338

  2. Conifers have a unique small RNA silencing signature

    PubMed Central

    Dolgosheina, Elena V.; Morin, Ryan D.; Aksay, Gozde; Sahinalp, S. Cenk; Magrini, Vincent; Mardis, Elaine R.; Mattsson, Jim; Unrau, Peter J.

    2008-01-01

    Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as RNA silencing. While RNA silencing has been extensively studied across the different phyla of the animal kingdom (e.g., mouse, fly, worm), similar studies in the plant kingdom have focused primarily on angiosperms, thus limiting evolutionary studies of RNA silencing in plants. Here we report on an unexpected phylogenetic difference in the size distribution of small RNAs among the vascular plants. By extracting total RNA from freshly growing shoot tissue, we conducted a survey of small RNAs in 24 vascular plant species. We find that conifers, which radiated from the other seed-bearing plants ∼260 million years ago, fail to produce significant amounts of 24-nucleotide (nt) RNAs that are known to guide DNA methylation and heterochromatin formation in angiosperms. Instead, they synthesize a diverse population of small RNAs that are exactly 21-nt long. This finding was confirmed by high-throughput sequencing of the small RNA sequences from a conifer, Pinus contorta. A conifer EST search revealed the presence of a novel Dicer-like (DCL) family, which may be responsible for the observed change in small RNA expression. No evidence for DCL3, an enzyme that matures 24-nt RNAs in angiosperms, was found. We hypothesize that the diverse class of 21-nt RNAs found in conifers may help to maintain organization of their unusually large genomes. PMID:18566193

  3. Wheat EST resources for functional genomics of abiotic stress

    PubMed Central

    Houde, Mario; Belcaid, Mahdi; Ouellet, François; Danyluk, Jean; Monroy, Antonio F; Dryanova, Ani; Gulick, Patrick; Bergeron, Anne; Laroche, André; Links, Matthew G; MacCarthy, Luke; Crosby, William L; Sarhan, Fathey

    2006-01-01

    Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals. PMID

  4. openSNP–A Crowdsourced Web Resource for Personal Genomics

    PubMed Central

    Greshake, Bastian; Bayer, Philipp E.; Rausch, Helge; Reda, Julia

    2014-01-01

    Genome-Wide Association Studies are widely used to correlate phenotypic traits with genetic variants. These studies usually compare the genetic variation between two groups to single out certain Single Nucleotide Polymorphisms (SNPs) that are linked to a phenotypic variation in one of the groups. However, it is necessary to have a large enough sample size to find statistically significant correlations. Direct-To-Consumer (DTC) genetic testing can supply additional data: DTC-companies offer the analysis of a large amount of SNPs for an individual at low cost without the need to consult a physician or geneticist. Over 100,000 people have already been genotyped through Direct-To-Consumer genetic testing companies. However, this data is not public for a variety of reasons and thus cannot be used in research. It seems reasonable to create a central open data repository for such data. Here we present the web platform openSNP, an open database which allows participants of Direct-To-Consumer genetic testing to publish their genetic data at no cost along with phenotypic information. Through this crowdsourced effort of collecting genetic and phenotypic information, openSNP has become a resource for a wide area of studies, including Genome-Wide Association Studies. openSNP is hosted at http://www.opensnp.org, and the code is released under MIT-license at http://github.com/gedankenstuecke/snpr. PMID:24647222

  5. The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer.

    PubMed

    Strausberg, R L

    2001-09-01

    The Cancer Genome Anatomy Project (CGAP) has built informational, technological, and physical resources to interface genomics with basic and clinical cancer research. The CGAP web site (http://cgap.nci.nih.gov) provides informatics tools for in silico analysis of the CGAP datasets as well as information for accessing each of the CGAP resources. Published in 2001 by John Wiley & Sons, Ltd.

  6. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

    PubMed

    Arnaud, Martha B; Chibucos, Marcus C; Costanzo, Maria C; Crabtree, Jonathan; Inglis, Diane O; Lotia, Adil; Orvis, Joshua; Shah, Prachi; Skrzypek, Marek S; Binkley, Gail; Miyasato, Stuart R; Wortman, Jennifer R; Sherlock, Gavin

    2010-01-01

    The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu.

  7. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome.

    PubMed

    Sjödin, Andreas; Street, Nathaniel Robert; Sandberg, Göran; Gustafsson, Petter; Jansson, Stefan

    2009-06-01

    Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info.

  8. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.

    PubMed

    Arnaud, Martha B; Cerqueira, Gustavo C; Inglis, Diane O; Skrzypek, Marek S; Binkley, Jonathan; Chibucos, Marcus C; Crabtree, Jonathan; Howarth, Clinton; Orvis, Joshua; Shah, Prachi; Wymore, Farrell; Binkley, Gail; Miyasato, Stuart R; Simison, Matt; Sherlock, Gavin; Wortman, Jennifer R

    2012-01-01

    The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review of the entire published literature about Aspergillus nidulans and Aspergillus fumigatus, and this annotation is provided with streamlined, ortholog-based navigation of the multispecies information. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. AspGD also provides resources to foster interaction and dissemination of community information and resources. We welcome and encourage feedback at aspergillus-curator@lists.stanford.edu.

  9. Genomic resources and their influence on the detection of the signal of positive selection in genome scans.

    PubMed

    Manel, S; Perrier, C; Pratlong, M; Abi-Rached, L; Paganini, J; Pontarotti, P; Aurelle, D

    2016-01-01

    Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful, for example, in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing exponentially, improving genome scan analyses in non-model species. Thousands of SNPs called using Reduced Representation Sequencing are increasingly used in genome scans. Besides, genome sequences are also becoming increasingly available, allowing better processing of short-read data, offering physical localization of variants, and improving haplotype reconstruction and data imputation. Ultimately, genome sequences are also becoming the raw material for selection inferences. Here, we discuss how the increasing availability of such genomic resources, notably genome sequences, influences the detection of signals of selection. Mainly, increasing data density and having the information of physical linkage data expand genome scans by (i) improving the overall quality of the data, (ii) helping the reconstruction of demographic history for the population studied to decrease false-positive rates and (iii) improving the statistical power of methods to detect the signal of selection. Of particular importance, the availability of a high-quality reference genome can improve the detection of the signal of selection by (i) allowing matching the potential candidate loci to linked coding regions under selection, (ii) rapidly moving the investigation to the gene and function and (iii) ensuring that the highly variable regions of the genomes that include functional genes are also investigated. For all those reasons, using reference genomes in genome scan analyses is highly recommended.

  10. An EST dataset for Metasequoia glyptostroboides buds: the first EST resource for molecular genomics studies in Metasequoia.

    PubMed

    Zhao, Ying; Thammannagowda, Shivegowda; Staton, Margaret; Tang, Sha; Xia, Xinli; Yin, Weilun; Liang, Haiying

    2013-03-01

    The "living fossil" Metasequoia glyptostroboides Hu et Cheng, commonly known as dawn redwood or Chinese redwood, is the only living species in the genus and is valued for its essential oil and crude extracts that have great potential for anti-fungal activity. Despite its paleontological significance and economical value as a rare relict species, genomic resources of Metasequoia are very limited. In order to gain insight into the molecular mechanisms behind the formation of reproductive buds and the transition from vegetative phase to reproductive phase in Metasequoia, we performed sequencing of expressed sequence tags from Metasequoia vegetative buds and female buds. By using the 454 pyrosequencing technology, a total of 1,571,764 high-quality reads were generated, among which 733,128 were from vegetative buds and 775,636 were from female buds. These EST reads were clustered and assembled into 114,124 putative unique transcripts (PUTs) with an average length of 536 bp. The 97,565 PUTs that were at least 100 bp in length were functionally annotated by a similarity search against public databases and assigned with Gene Ontology (GO) terms. A total of 59 known floral gene families and 190 isotigs involved in hormone regulation were captured in the dataset. Furthermore, a set of PUTs differentially expressed in vegetative and reproductive buds, as well as SSR motifs and high confidence SNPs, were identified. This is the first large-scale expressed sequence tags ever generated in Metasequoia and the first evidence for floral genes in this critically endangered deciduous conifer species.

  11. CucCAP - Developing genomic resources for the cucurbit community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. cucurbit community has initiated a USDA-SCRI funded cucurbit genomics project, CucCAP: Leveraging applied genomics to increase disease resistance in cucurbit crops. Our primary objectives are: develop genomic and bioinformatic breeding tool kits for accelerated crop improvement across the...

  12. Ecophysiological controls of conifer distributions

    SciTech Connect

    Woodward, F.I.

    1995-07-01

    The boreal forest covers the most extensive worldwide area of conifer-dominated vegetation, with a total global area of about 12 million km{sup 2}. This large area is very species poor; in North America there are only nine widespread and dominant species of trees, of which six are conifers-Picea mariana, Picea glauca, Abies balsamea, Larix laricina, Pinus contorta, and Pinus banksiana. The remaining three angiosperms are Betula papyrifera, Populus tremuloides, and Populus balsamifera. In Fennoscandia and the former Soviet Union, 14 species dominate the boreal forest, 10 of which are conifers-Abies sibirica, Larix gmelinii, Larix sibirica, Larix sukaczewii, Picea abies, Picea ajanensis, Picea obovata, Pinus pumila, Pinus sibifica, and Pinus sylvestris. The dominant angiosperm trees are Betula pendula, Betula pubescens, Chosenia arbutifolia, and Populus tremula. Such species paucity detracts from realizing the remarkable capacity of these species to endure the harshest forest climates of the world. Both the short-term geological history and the current climate are major causes of the species paucity in the boreal forest. In general, the boreal forest has been present in its current distribution only since the Holocene era. In most cases, the dominant species of the boreal forest completed their postglacial expansion to their current distributions only over the past 2000 years. So the ecology of the forest is very young, in comparison with forests in warmer climates. It might be expected that over subsequent millennia, with no climatic change, there could be a slow influx of new species to the boreal zone; however, the extreme climatic, edaphic, and disturbance characteristics of the area are likely to set insurmountable limits on this influx of diversity.

  13. De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis.

    PubMed

    Hu, Xian-Ge; Liu, Hui; Jin, YuQing; Sun, Yan-Qiang; Li, Yue; Zhao, Wei; El-Kassaby, Yousry A; Wang, Xiao-Ru; Mao, Jian-Feng

    2016-01-01

    Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs. PMID:26881995

  14. De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis

    PubMed Central

    Jin, YuQing; Sun, Yan-Qiang; Li, Yue; Zhao, Wei; El-Kassaby, Yousry A.; Wang, Xiao-Ru; Mao, Jian-Feng

    2016-01-01

    Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species’ genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs. PMID:26881995

  15. Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement.

    PubMed

    Bohra, Abhishek; Singh, Narendra P

    2015-08-01

    Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.

  16. Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard

    PubMed Central

    Overby, Casey Lynnette; Del Fiol, Guilherme; Rubinstein, Wendy S.; Maglott, Donna R.; Nelson, Tristan H.; Milosavljevic, Aleksandar; Martin, Christa L.; Goehringer, Scott R.; Freimuth, Robert R.; Williams, Marc S.

    2016-01-01

    Summary Background The Clinical Genome Resource (ClinGen) Electronic Health Record (EHR) Workgroup aims to integrate ClinGen resources with EHRs. A promising option to enable this integration is through the Health Level Seven (HL7) Infobutton Standard. EHR systems that are certified according to the US Meaningful Use program provide HL7-compliant infobutton capabilities, which can be leveraged to support clinical decision-making in genomics. Objectives To integrate genomic knowledge resources using the HL7 infobutton standard. Two tactics to achieve this objective were: (1) creating an HL7-compliant search interface for ClinGen, and (2) proposing guidance for genomic resources on achieving HL7 Infobutton standard accessibility and compliance. Methods We built a search interface utilizing OpenInfobutton, an open source reference implementation of the HL7 Infobutton standard. ClinGen resources were assessed for readiness towards HL7 compliance. Finally, based upon our experiences we provide recommendations for publishers seeking to achieve HL7 compliance. Results Eight genomic resources and two sub-resources were integrated with the ClinGen search engine via OpenInfobutton and the HL7 infobutton standard. Resources we assessed have varying levels of readiness towards HL7-compliance. Furthermore, we found that adoption of standard terminologies used by EHR systems is the main gap to achieve compliance. Conclusion Genomic resources can be integrated with EHR systems via the HL7 Infobutton standard using OpenInfobutton. Full compliance of genomic resources with the Infobutton standard would further enhance interoperability with EHR systems. PMID:27579472

  17. Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

    PubMed Central

    Matsukura, C; Aoki, K; Fukuda, N; Mizoguchi, T; Asamizu, E; Saito, T; Shibata, D; Ezura, H

    2008-01-01

    Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom. PMID:19506732

  18. Evidence of Intense Chromosomal Shuffling during Conifer Evolution

    PubMed Central

    de Miguel, Marina; Bartholomé, Jérôme; Ehrenmann, François; Murat, Florent; Moriguchi, Yoshinari; Uchiyama, Kentaro; Ueno, Saneyoshi; Tsumura, Yoshihiko; Lagraulet, Hélène; de Maria, Nuria; Cabezas, José-Antonio; Cervera, María-Teresa; Gion, Jean Marc; Salse, Jérôme; Plomion, Christophe

    2015-01-01

    Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes. PMID:26400405

  19. Defense Mechanisms of Conifers 1

    PubMed Central

    Lewinsohn, Efraim; Gijzen, Mark; Savage, Thomas J.; Croteau, Rodney

    1991-01-01

    Cell-free extracts from Pinus ponderosa Lawson (ponderosa pine) and Pinus sylvestris L. (Scotch pine) wood exhibited high levels of monoterpene synthase (cyclase) activity, whereas bark extracts of these species contained no detectable activity, and they inhibited cyclase activity when added to extracts from wood, unless polyvinylpyrrolidone was included in the preparation. The molecular mass of the polyvinylpyrrolidone added was of little consequence; however, polyvinylpolypyrrolidone (a cross-linked insoluble form of the polymer) was ineffective in protecting enzyme activity. Based on these observations, methods were developed for the efficient extraction and assay of monoterpene cyclase activity from conifer stem (wood and bark) tissue. The level of monoterpene cyclase activity for a given conifer species was shown to correlate closely with the monoterpene content of the oleoresin and with the degree of anatomical complexity of the specialized resin-secreting structures. Cyclase activity and monoterpene content were lowest in the stems of species containing only isolated resin cells, such as western red cedar (Thuja plicata D. Don). Increasing levels of cyclase activity and oleoresin monoterpenes were observed in advancing from species with multicellular resin blisters (true firs [Abies]) to those with organized resin passages, such as western larch (Larix occidentalis Nutt.), Colorado blue spruce (Picea pungens Engelm.) and Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). The highest levels of cyclase activity and oleoresin monoterpenes were noted in Pinus species that contain the most highly developed resin duct systems. The relationship between biosynthetic capacity, as measured by cyclase activity, monoterpene content, and the degree of organization of the secretory structures for a given species, may reflect the total number of specialized resin-producing cells per unit mass of stem tissue. PMID:16668182

  20. SchistoDB: a Schistosoma mansoni genome resource

    PubMed Central

    Zerlotini, Adhemar; Heiges, Mark; Wang, Haiming; Moraes, Romulo L. V.; Dominitini, Anderson J.; Ruiz, Jerônimo C.; Kissinger, Jessica C.; Oliveira, Guilherme

    2009-01-01

    SchistoDB (http://schistoDB.net/) is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. In this article, we describe the data sets and its analyses, how to query the database and tools available in the website. PMID:18842636

  1. Megx.net: integrated database resource for marine ecological genomics.

    PubMed

    Kottmann, Renzo; Kostadinov, Ivalyo; Duhaime, Melissa Beth; Buttigieg, Pier Luigi; Yilmaz, Pelin; Hankeln, Wolfgang; Waldmann, Jost; Glöckner, Frank Oliver

    2010-01-01

    Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.

  2. Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

    PubMed

    Hirschman, Jodi E; Balakrishnan, Rama; Christie, Karen R; Costanzo, Maria C; Dwight, Selina S; Engel, Stacia R; Fisk, Dianna G; Hong, Eurie L; Livstone, Michael S; Nash, Robert; Park, Julie; Oughtred, Rose; Skrzypek, Marek; Starr, Barry; Theesfeld, Chandra L; Williams, Jennifer; Andrada, Rey; Binkley, Gail; Dong, Qing; Lane, Christopher; Miyasato, Stuart; Sethuraman, Anand; Schroeder, Mark; Thanawala, Mayank K; Weng, Shuai; Dolinski, Kara; Botstein, David; Cherry, J Michael

    2006-01-01

    Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on an ongoing basis, the Saccharomyces Genome Database (SGD) (http://www.yeastgenome.org/) has created the Genome Snapshot (http://db.yeastgenome.org/cgi-bin/genomeSnapShot.pl). The Genome Snapshot summarizes the current state of knowledge about the genes and chromosomal features of S.cerevisiae. The information is organized into two categories: (i) number of each type of chromosomal feature annotated in the genome and (ii) number and distribution of genes annotated to Gene Ontology terms. Detailed lists are accessible through SGD's Advanced Search tool (http://db.yeastgenome.org/cgi-bin/search/featureSearch), and all the data presented on this page are available from the SGD ftp site (ftp://ftp.yeastgenome.org/yeast/).

  3. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

    PubMed

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/.

  4. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources

    PubMed Central

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/ PMID:26589635

  5. An Italian functional genomic resource for Medicago truncatula

    PubMed Central

    Porceddu, Andrea; Panara, Francesco; Calderini, Ornella; Molinari, Lorna; Taviani, Paola; Lanfaloni, Luisa; Scotti, Carla; Carelli, Maria; Scaramelli, Laura; Bruschi, Gianluca; Cosson, Viviane; Ratet, Pascal; de Larembergue, Henri; Duc, Gerard; Piano, Efisio; Arcioni, Sergio

    2008-01-01

    Background Medicago truncatula is a model species for legumes. Its functional genomics have been considerably boosted in recent years due to initiatives based both in Europe and US. Collections of mutants are becoming increasingly available and this will help unravel the genetic control of important traits for many species of legumes. Findings Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States. PMID:19077311

  6. InsectBase: a resource for insect genomes and transcriptomes

    PubMed Central

    Yin, Chuanlin; Shen, Gengyu; Guo, Dianhao; Wang, Shuping; Ma, Xingzhou; Xiao, Huamei; Liu, Jinding; Zhang, Zan; Liu, Ying; Zhang, Yiqun; Yu, Kaixiang; Huang, Shuiqing; Li, Fei

    2016-01-01

    The genomes and transcriptomes of hundreds of insects have been sequenced. However, insect community lacks an integrated, up-to-date collection of insect gene data. Here, we introduce the first release of InsectBase, available online at http://www.insect-genome.com. The database encompasses 138 insect genomes, 116 insect transcriptomes, 61 insect gene sets, 36 gene families of 60 insects, 7544 miRNAs of 69 insects, 96 925 piRNAs of Drosophila melanogaster and Chilo suppressalis, 2439 lncRNA of Nilaparvata lugens, 22 536 pathways of 78 insects, 678 881 untranslated regions (UTR) of 84 insects and 160 905 coding sequences (CDS) of 70 insects. This release contains over 12 million sequences and provides search functionality, a BLAST server, GBrowse, insect pathway construction, a Facebook-like network for the insect community (iFacebook), and phylogenetic analysis of selected genes. PMID:26578584

  7. CyanoClust: comparative genome resources of cyanobacteria and plastids.

    PubMed

    Sasaki, Naobumi V; Sato, Naoki

    2010-01-01

    Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Proteins (COG). CyanoClust is a database of homolog groups in cyanobacteria and plastids that are produced by the program Gclust. We have developed a web-server system for the protein homology database featuring cyanobacteria and plastids. Database URL: http://cyanoclust.c.u-tokyo.ac.jp/.

  8. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

    SciTech Connect

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2009-09-13

    The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at .

  9. Comparative Plant Genomics Resources at PlantGDB1

    PubMed Central

    Dong, Qunfeng; Lawrence, Carolyn J.; Schlueter, Shannon D.; Wilkerson, Matthew D.; Kurtz, Stefan; Lushbough, Carol; Brendel, Volker

    2005-01-01

    PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database. PMID:16219921

  10. A Populus EST resource for plant functional genomics.

    PubMed

    Sterky, Fredrik; Bhalerao, Rupali R; Unneberg, Per; Segerman, Bo; Nilsson, Peter; Brunner, Amy M; Charbonnel-Campaa, Laurence; Lindvall, Jenny Jonsson; Tandre, Karolina; Strauss, Steven H; Sundberg, Björn; Gustafsson, Petter; Uhlén, Mathias; Bhalerao, Rishikesh P; Nilsson, Ove; Sandberg, Göran; Karlsson, Jan; Lundeberg, Joakim; Jansson, Stefan

    2004-09-21

    Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

  11. StaphyloBase: a specialized genomic resource for the staphylococcal research community.

    PubMed

    Heydari, Hamed; Mutha, Naresh V R; Mahmud, Mahafizul Imran; Siow, Cheuk Chuen; Wee, Wei Yee; Wong, Guat Jah; Yazdi, Amir Hessam; Ang, Mia Yang; Choo, Siew Woh

    2014-01-01

    With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/.

  12. Genomic Resources Notes Accepted 1 August 2015 - 31 September 2015.

    PubMed

    Kohler, Annegret; Kremer, Antoine; Le Provost, Grégoire; Lesur, Isabelle; Lin, Gonhua; Martin, Francis; Plomion, Christophe; Wu, Aiguo; Zhao, Fang

    2016-01-01

    This article documents the public availability of transcriptomic resources for (i) the Hazelnut tree (Corylus avellana L.) and (ii) the oriental rat flea and primary plague vector, Xenopsylla cheopis. PMID:26768197

  13. Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa)

    PubMed Central

    Chen, Kefei; Baxter, Tara; Muir, William M.; Groenen, Martien A.; Schook, Lawrence B.

    2007-01-01

    The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health. PMID:17384734

  14. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

    PubMed Central

    2010-01-01

    While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores. PMID:20398345

  15. e-Fungi: a data resource for comparative analysis of fungal genomes

    PubMed Central

    Hedeler, Cornelia; Wong, Han Min; Cornell, Michael J; Alam, Intikhab; Soanes, Darren M; Rattray, Magnus; Hubbard, Simon J; Talbot, Nicholas J; Oliver, Stephen G; Paton, Norman W

    2007-01-01

    Background The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example using techniques from functional genomics. Comparative analysis has proven to be a useful strategy for enhancing our understanding of evolutionary biology and of the less well understood genomes. However, the data required for these analyses tends to be distributed in various heterogeneous data sources, making systematic comparative studies a cumbersome task. Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species. Description To support systematic comparative analyses of fungal genomes we have developed the e-Fungi database, which integrates a variety of data for more than 30 fungal genomes. Publicly available genome data, functional annotations, and pathway information has been integrated into a single data repository and complemented with results of comparative analyses, such as MCL and OrthoMCL cluster analysis, and predictions of signaling proteins and the sub-cellular localisation of proteins. To access the data, a library of analysis tasks is available through a web interface. The analysis tasks are motivated by recent comparative genomics studies, and aim to support the study of evolutionary biology as well as community efforts for improving the annotation of genomes. Web services for each query are also available, enabling the tasks to be incorporated into workflows. Conclusion The e-Fungi database provides fungal biologists with a resource for comparative studies of a large range of fungal genomes. Its analysis library supports the comparative study of genome data, functional annotation, and results of large scale analyses over all the genomes stored in the database

  16. Infrared radiation from hot cones on cool conifers attracts seed-feeding insects

    PubMed Central

    Takács, Stephen; Bottomley, Hannah; Andreller, Iisak; Zaradnik, Tracy; Schwarz, Joseph; Bennett, Robb; Strong, Ward; Gries, Gerhard

    2008-01-01

    Foraging animals use diverse cues to locate resources. Common foraging cues have visual, auditory, olfactory, tactile or gustatory characteristics. Here, we show a foraging herbivore using infrared (IR) radiation from living plants as a host-finding cue. We present data revealing that (i) conifer cones are warmer and emit more near-, mid- and long-range IR radiation than needles, (ii) cone-feeding western conifer seed bugs, Leptoglossus occidentalis (Hemiptera: Coreidae), possess IR receptive organs and orient towards experimental IR cues, and (iii) occlusion of the insects' IR receptors impairs IR perception. The conifers' cost of attracting cone-feeding insects may be offset by occasional mast seeding resulting in cone crops too large to be effectively exploited by herbivores. PMID:18945664

  17. Infrared radiation from hot cones on cool conifers attracts seed-feeding insects.

    PubMed

    Takács, Stephen; Bottomley, Hannah; Andreller, Iisak; Zaradnik, Tracy; Schwarz, Joseph; Bennett, Robb; Strong, Ward; Gries, Gerhard

    2009-02-22

    Foraging animals use diverse cues to locate resources. Common foraging cues have visual, auditory, olfactory, tactile or gustatory characteristics. Here, we show a foraging herbivore using infrared (IR) radiation from living plants as a host-finding cue. We present data revealing that (i) conifer cones are warmer and emit more near-, mid- and long-range IR radiation than needles, (ii) cone-feeding western conifer seed bugs, Leptoglossus occidentalis (Hemiptera: Coreidae), possess IR receptive organs and orient towards experimental IR cues, and (iii) occlusion of the insects' IR receptors impairs IR perception. The conifers' cost of attracting cone-feeding insects may be offset by occasional mast seeding resulting in cone crops too large to be effectively exploited by herbivores.

  18. The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

    PubMed

    Eppig, Janan T; Bult, Carol J; Kadin, James A; Richardson, Joel E; Blake, Judith A; Anagnostopoulos, A; Baldarelli, R M; Baya, M; Beal, J S; Bello, S M; Boddy, W J; Bradt, D W; Burkart, D L; Butler, N E; Campbell, J; Cassell, M A; Corbani, L E; Cousins, S L; Dahmen, D J; Dene, H; Diehl, A D; Drabkin, H J; Frazer, K S; Frost, P; Glass, L H; Goldsmith, C W; Grant, P L; Lennon-Pierce, M; Lewis, J; Lu, I; Maltais, L J; McAndrews-Hill, M; McClellan, L; Miers, D B; Miller, L A; Ni, L; Ormsby, J E; Qi, D; Reddy, T B K; Reed, D J; Richards-Smith, B; Shaw, D R; Sinclair, R; Smith, C L; Szauter, P; Walker, M B; Walton, D O; Washburn, L L; Witham, I T; Zhu, Y

    2005-01-01

    The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

  19. CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips.

    PubMed

    Heydari, Hamed; Siow, Cheuk Chuen; Tan, Mui Fern; Jakubovics, Nick S; Wee, Wei Yee; Mutha, Naresh V R; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam; Choo, Siew Woh

    2014-01-01

    Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.

  20. MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

    PubMed

    Uchiyama, Ikuo; Higuchi, Toshio; Kawai, Mikihiko

    2010-01-01

    The microbial genome database (MBGD) for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature of MBGD is that it allows users to create ortholog groups using a specified subgroup of organisms. The database is constantly updated and now contains almost 1000 genomes. To utilize the MBGD database as a comprehensive resource for investigating microbial genome diversity, we have developed the following advanced functionalities: (i) enhanced assignment of functional annotation, including external database links to each orthologous group, (ii) interface for choosing a set of genomes to compare based on phenotypic properties, (iii) the addition of more eukaryotic microbial genomes (fungi and protists) and some higher eukaryotes as references and (iv) enhancement of the MyMBGD mode, which allows users to add their own genomes to MBGD and now accepts raw genomic sequences without any annotation (in such a case, it runs a gene-finding procedure before identifying the orthologs). Some analysis functions, such as the function to find orthologs with similar phylogenetic patterns, have also been improved. MBGD is accessible at http://mbgd.genome.ad.jp/.

  1. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

    PubMed

    Bracken-Grissom, Heather; Collins, Allen G; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Mónica; Messing, Charles; O'Brien, Stephen J; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W; Ryan, Joseph F; Schulze, Anja; Wörheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E; Diaz, M Christina; Evans, Nathaniel; Flot, Jean-François; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y; Laberge, Tammy; Lavrov, Dennis; Michonneau, François; Moroz, Leonid L; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A; Rhodes, Adelaide; Santos, Scott R; Satoh, Nori; Thacker, Robert W; Van de Peer, Yves; Voolstra, Christian R; Welch, David Mark; Winston, Judith; Zhou, Xin

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.

  2. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    PubMed Central

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  3. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

    PubMed

    Bracken-Grissom, Heather; Collins, Allen G; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Mónica; Messing, Charles; O'Brien, Stephen J; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W; Ryan, Joseph F; Schulze, Anja; Wörheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E; Diaz, M Christina; Evans, Nathaniel; Flot, Jean-François; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y; Laberge, Tammy; Lavrov, Dennis; Michonneau, François; Moroz, Leonid L; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A; Rhodes, Adelaide; Santos, Scott R; Satoh, Nori; Thacker, Robert W; Van de Peer, Yves; Voolstra, Christian R; Welch, David Mark; Winston, Judith; Zhou, Xin

    2014-01-01

    Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture. PMID:24336862

  4. Update on Genomic Databases and Resources at the National Center for Biotechnology Information.

    PubMed

    Tatusova, Tatiana

    2016-01-01

    The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data.

  5. Update on Genomic Databases and Resources at the National Center for Biotechnology Information.

    PubMed

    Tatusova, Tatiana

    2016-01-01

    The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data. PMID:27115625

  6. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

    PubMed

    McNeil, Leslie Klis; Reich, Claudia; Aziz, Ramy K; Bartels, Daniela; Cohoon, Matthew; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Hwang, Kaitlyn; Kubal, Michael; Margaryan, Gohar Rem; Meyer, Folker; Mihalo, William; Olsen, Gary J; Olson, Robert; Osterman, Andrei; Paarmann, Daniel; Paczian, Tobias; Parrello, Bruce; Pusch, Gordon D; Rodionov, Dmitry A; Shi, Xinghua; Vassieva, Olga; Vonstein, Veronika; Zagnitko, Olga; Xia, Fangfang; Zinner, Jenifer; Overbeek, Ross; Stevens, Rick

    2007-01-01

    The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of approximately 50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development. PMID:17145713

  7. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

    PubMed Central

    McNeil, Leslie Klis; Reich, Claudia; Aziz, Ramy K.; Bartels, Daniela; Cohoon, Matthew; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Hwang, Kaitlyn; Kubal, Michael; Margaryan, Gohar Rem; Meyer, Folker; Mihalo, William; Olsen, Gary J.; Olson, Robert; Osterman, Andrei; Paarmann, Daniel; Paczian, Tobias; Parrello, Bruce; Pusch, Gordon D.; Rodionov, Dmitry A.; Shi, Xinghua; Vassieva, Olga; Vonstein, Veronika; Zagnitko, Olga; Xia, Fangfang; Zinner, Jenifer; Overbeek, Ross; Stevens, Rick

    2007-01-01

    The National Microbial Pathogen Data Resource (NMPDR) () is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of ∼50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development. PMID:17145713

  8. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.

    PubMed

    Bruford, Michael W; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J; Amaral, Andreia J; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F; Hall, Stephen J G; Hanotte, Olivier; Hassan, Faiz-Ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

    2015-01-01

    Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are

  9. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.

    PubMed

    Bruford, Michael W; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J; Amaral, Andreia J; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F; Hall, Stephen J G; Hanotte, Olivier; Hassan, Faiz-Ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

    2015-01-01

    Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are

  10. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

    PubMed Central

    Bruford, Michael W.; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J.; Amaral, Andreia J.; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F.; Hall, Stephen J. G.; Hanotte, Olivier; Hassan, Faiz-ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L.; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

    2015-01-01

    Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are

  11. A whole-genome, radiation hybrid mapping resource of hexaploid wheat.

    PubMed

    Tiwari, Vijay K; Heesacker, Adam; Riera-Lizarazu, Oscar; Gunn, Hilary; Wang, Shichen; Wang, Yi; Gu, Young Q; Paux, Etienne; Koo, Dal-Hoe; Kumar, Ajay; Luo, Ming-Cheng; Lazo, Gerard; Zemetra, Robert; Akhunov, Eduard; Friebe, Bernd; Poland, Jesse; Gill, Bikram S; Kianian, Shahryar; Leonard, Jeffrey M

    2016-04-01

    Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.

  12. STINGRAY: system for integrated genomic resources and analysis

    PubMed Central

    2014-01-01

    Background The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/. PMID:24606808

  13. A genome-scale shRNA resource for transgenic RNAi in Drosophila.

    PubMed

    Ni, Jian-Quan; Zhou, Rui; Czech, Benjamin; Liu, Lu-Ping; Holderbaum, Laura; Yang-Zhou, Donghui; Shim, Hye-Seok; Tao, Rong; Handler, Dominik; Karpowicz, Phillip; Binari, Richard; Booker, Matthew; Brennecke, Julius; Perkins, Lizabeth A; Hannon, Gregory J; Perrimon, Norbert

    2011-05-01

    Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource. PMID:21460824

  14. An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.

    PubMed

    Lin, Xuan; Faridi, Nurul; Casola, Claudio

    2016-01-01

    Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants. PMID:27190138

  15. An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers

    PubMed Central

    Lin, Xuan; Faridi, Nurul; Casola, Claudio

    2016-01-01

    Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants. PMID:27190138

  16. Final progress report, Construction of a genome-wide highly characterized clone resource for genome sequencing

    SciTech Connect

    Nierman, William C.

    2000-02-14

    At TIGR, the human Bacterial Artificial Chromosome (BAC) end sequencing and trimming were with an overall sequencing success rate of 65%. CalTech human BAC libraries A, B, C and D as well as Roswell Park Cancer Institute's library RPCI-11 were used. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length {approx}460 bp for a total of 141 Mb covering {approx}4.7% of the genome. Over sixty percent of the clones have BAC end sequences (BESs) from both ends representing over five-fold coverage of the genome by the paired-end clones. The average phred Q20 length is {approx}400 bp. This high accuracy makes our BESs match the human finished sequences with an average identity of 99% and a match length of 450 bp, and a frequency of one match per 12.8 kb contig sequence. Our sample tracking has ensured a clone tracking accuracy of >90%, which gives researchers a high confidence in (1) retrieving the right clone from the BA C libraries based on the sequence matches; and (2) building a minimum tiling path of sequence-ready clones across the genome and genome assembly scaffolds.

  17. Genomic resources for multiple species in the Drosophila ananassae species group.

    PubMed

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa. PMID:23639891

  18. Genomic resources for multiple species in the Drosophila ananassae species group

    PubMed Central

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa. PMID:23639891

  19. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

    PubMed

    Megy, Karine; Emrich, Scott J; Lawson, Daniel; Campbell, David; Dialynas, Emmanuel; Hughes, Daniel S T; Koscielny, Gautier; Louis, Christos; Maccallum, Robert M; Redmond, Seth N; Sheehan, Andrew; Topalis, Pantelis; Wilson, Derek

    2012-01-01

    VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community. PMID:22135296

  20. Genome-scale resources for Thermoanaerobacterium saccharolyticum

    SciTech Connect

    Currie, Devin H.; Raman, Babu; Gowen, Christopher M.; Tschaplinski, Timothy J.; Land, Miriam L.; Brown, Steven D.; Covalla, Sean; Klingeman, Dawn Marie; Yang, Zamin Koo; Engle, Nancy L.; Johnson, Courtney M.; Rodriguez, Miguel A.; Shaw, A. Joe; Kenealy, William R.; Lynd, Lee R.; Fong, Stephen S.; Mielenz, Jonathan R.; Davison, Brian H.; Hogsett, David A.; Herring, Christopher D.

    2015-06-26

    Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. For this research, a major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation.

  1. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

    PubMed Central

    Pipes, Lenore; Li, Sheng; Bozinoski, Marjan; Palermo, Robert; Peng, Xinxia; Blood, Phillip; Kelly, Sara; Weiss, Jeffrey M.; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Zumbo, Paul; Chen, Ronghua; Schroth, Gary P.; Mason, Christopher E.; Katze, Michael G.

    2013-01-01

    RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new information regarding gene and transcript structure, expression and regulation. This is particularly true for non-coding RNAs where whole transcriptome analyses have revealed that the much of the genome is transcribed and that many non-coding transcripts have widespread functionality. However, uniform resources for raw, cleaned and processed RNA-Seq data are sparse for most organisms and this is especially true for non-human primates (NHPs). Here, we describe a large-scale RNA-Seq data and analysis infrastructure, the NHP reference transcriptome resource (http://nhprtr.org); it presently hosts data from12 species of primates, to be expanded to 15 species/subspecies spanning great apes, old world monkeys, new world monkeys and prosimians. Data are collected for each species using pools of RNA from comparable tissues. We provide data access in advance of its deposition at NCBI, as well as browsable tracks of alignments against the human genome using the UCSC genome browser. This resource will continue to host additional RNA-Seq data, alignments and assemblies as they are generated over the coming years and provide a key resource for the annotation of NHP genomes as well as informing primate studies on evolution, reproduction, infection, immunity and pharmacology. PMID:23203872

  2. Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

    NASA Astrophysics Data System (ADS)

    Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

    2016-10-01

    Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

  3. Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

    PubMed Central

    Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

    2016-01-01

    Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications. PMID:27721449

  4. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    PubMed

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  5. Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

    PubMed Central

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  6. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    PubMed

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

  7. Natural and artificial mutants as valuable resources for functional genomics and molecular breeding.

    PubMed

    Jiang, Shu-Ye; Ramachandran, Srinivasan

    2010-01-01

    With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.

  8. Diseases of Pacific Coast conifers. Agriculture handbook

    SciTech Connect

    Scharpf, R.F.

    1993-06-01

    The handbook provides basic information needed to identify the common diseases of Pacific Coast conifers. Hosts, distribution, disease cycles, and identifying characteristics are described for more than 150 diseases, including cankers, diebacks, galls, rusts, needle diseases, root diseases, mistletoes, and rots. Diseases in which abiotic factors are involved are also described. For some groups of diseases, a descriptive key to field identification is included.

  9. Montane conifer fuel dynamics, Yosemite National Park

    USGS Publications Warehouse

    van Wagtendonk, J.W.; Moore, P.E.

    1997-01-01

    Litter and woody fuel accumulation rates over 7 years for 7 montane Sierra Nevada conifer species, including giant sequoia, ponderosa pine, sugar pine, Jeffrey pine, incense-cedar and white fir. Data are from four sites per size class per species with four size classes each. Nonspatial, georeferenced.

  10. Genetics and the physiological ecology of conifers

    SciTech Connect

    Mitton, J.B.

    1995-07-01

    Natural selection acts on the diversity of genotypes, adapting populations to their specific environments and driving evolution in response to changes in climate. Genetically based differences in physiology and demography adapt species to alternate environments and produce, along with historical accidents, the present distribution of species. The sorting of conifer species by elevation is so marked that conifers help to define plant communities arranged in elevational bands in the Rocky Mountains. For these reasons, a genetic perspective is necessary to appreciate the evolution of ecophysiological patterns in the coniferous forests of the Rocky Mountains. The fascinating natural history and the economic importance of western conifers have stimulated numerous studies of their ecology, ecological genetics, and geographic variation. These studies yield some generalizations, and present some puzzling contradictions. This chapter focuses on the genetic variability associated with the physiological differences among genotypes in Rocky Mountain conifers. Variation among genotypes in survival, growth, and resistance to herbivores is used to illustrate genetically based differences in physiology, and to suggest the mechanistic studies needed to understand the relationships between genetic and physiological variation.

  11. Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Reeve, Wayne

    2013-03-01

    Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  12. A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy.

    PubMed

    Brenton, Zachary W; Cooper, Elizabeth A; Myers, Mathew T; Boyles, Richard E; Shakoor, Nadia; Zielinski, Kelsey J; Rauh, Bradley L; Bridges, William C; Morris, Geoffrey P; Kresovich, Stephen

    2016-09-01

    With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.

  13. A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy

    PubMed Central

    Brenton, Zachary W.; Cooper, Elizabeth A.; Myers, Mathew T.; Boyles, Richard E.; Shakoor, Nadia; Zielinski, Kelsey J.; Rauh, Bradley L.; Bridges, William C.; Morris, Geoffrey P.; Kresovich, Stephen

    2016-01-01

    With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production

  14. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

    PubMed Central

    2014-01-01

    Background The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. Results We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome. Conclusions In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied. PMID:24647006

  15. Nuclear DNA content affects the productivity of conifer forests by altering hydraulic architecture

    NASA Astrophysics Data System (ADS)

    Alday, Josu; Resco de Dios, Víctor

    2014-05-01

    Predictions of future global climate rely on feedbacks between terrestrial vegetation and the global carbon cycle, but the exact mechanisms underlying this relationship are still being discussed. One of the key knowledge gaps lies on the scaling of cellular processes to the ecosystem level. Here we examine whether an under-explored plant trait, inter-specific variation in the bulk amount of DNA in unreplicated somatic cells (2C DNA content), can explain inter-specific variation in the maximum productivity of conifer forests. We expected 2C DNA content to be negatively related to conifer productivity because: 1) it is positively correlated with cell volume (which, in turn, potentially affects structural features such as leaf mass area, a strong predictor of photosynthetic capacity); 2) it is positively correlated with stomatal size (with larger stomata leading to lower overall stomatal conductance and, by extension, lower CO2 uptake); and 3) larger genome sizes may reduce P availability in RNA (which has been hypothesized to slow growth). We present the results of regression and independent contrasts in different monospecific forests encompassing a 52º latitudinal gradient, each being dominated by 1 of 35 different conifer species. Contrary to expectations, we observed a positive correlation between genome size and maximum Gross Primary Productivity (R2 = 0.47) and also between genome size maximum tree height (R2 = 0.27). This correlation was apparently driven by the effects of genome size on stem hydraulics, since 2C DNA was positively correlated with wood density (R2 = 0.40) and also with resistance to cavitation (P50, R2 = 0.28). That is, increased genome sizes have a positive effect on the productivity of conifer forests by affecting the vascular tissues to increase their capacity for water transport. Our results shed a new light on the evolution of the vascular system of conifer forests and how they affect ecosystem productivity, and indicate the potential to

  16. Preterm Birth Genome Project (PGP) -- validation of resources for preterm birth genome-wide studies.

    PubMed

    Pennell, Craig E; Vadillo-Ortega, Felipe; Olson, David M; Ha, Eun-Hee; Williams, Scott; Frayling, Tim M; Dolan, Siobhan; Katz, Michael; Merialdi, Mario; Menon, Ramkumar

    2013-01-01

    We determined a series of quality control (QC) analyses to assess the usability of DNA collected and processed from different countries utilizing different DNA extraction techniques prior to genome-wide association studies (GWAS). The quality of DNA collected utilizing four different DNA extraction techniques and the impact of shipping DNA at different temperatures on array performance were evaluated. Fifteen maternal-fetal pairs were used from four countries. DNA was extracted using four approaches: whole blood, blood spots with whole genome amplification (WGA), saliva and buccal swab. Samples were sent to a genotyping facility, either on dry ice or at room temperature and genotyped using Affymetrix SNP array 6.0. QC measured included extraction techniques, effect of shipping temperatures, accuracy and Mendelian concordance. Significantly fewer (50 % ) single nucleotide polymorphisms (SNPs) passed QC metrics for buccal swab DNA (P < 0.0001) due to missing genotype data (P < 0.0001). Whole blood or saliva DNA had the highest call rates (99.2 0.4 % and 99.3 0.2 % , respectively) and Mendelian concordance. Shipment temperature had no effect. DNA from blood or saliva had the highest call rate accuracy, and buccal swabs had the lowest. DNA extracted from blood, saliva and blood spots were found suitable for GWAS in our study.

  17. Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.

    PubMed

    Megy, K; Hammond, M; Lawson, D; Bruggner, R V; Birney, E; Collins, F H

    2009-05-01

    High-throughput genome sequencing techniques have now reached vector biology with an emphasis on those species that are vectors of human pathogens. The first mosquito to be sequenced was Anopheles gambiae, the vector for Plasmodium parasites that cause malaria. Further mosquitoes have followed: Aedes aegypti (yellow fever and dengue fever vector) and Culex pipiens (lymphatic filariasis and West Nile fever). Species that are currently in sequencing include the body louse Pediculus humanus (Typhus vector), the triatomine Rhodnius prolixus (Chagas disease vector) and the tick Ixodes scapularis (Lyme disease vector). The motivations for sequencing vector genomes are to further understand vector biology, with an eye on developing new control strategies (for example novel chemical attractants or repellents) or understanding the limitations of current strategies (for example the mechanism of insecticide resistance); to analyse the mechanisms driving their evolution; and to perform an exhaustive analysis of the gene repertory. The proliferation of genomic data creates the need for efficient and accessible storage. We present VectorBase, a genomic resource centre that is both involved in the annotation of vector genomes and act as a portal for access to the genomic information (http://www.vectorbase.org).

  18. Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus).

    PubMed

    Thanh, Nguyen Minh; Jung, Hyungtaek; Lyons, Russell E; Njaci, Isaac; Yoon, Byoung-Ha; Chand, Vincent; Tuan, Nguyen Viet; Thu, Vo Thi Minh; Mather, Peter

    2015-10-01

    Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species. PMID:25979246

  19. Utilizing Genomics to Study Entomopathogenicity in the Fungal Phylum Entomophthoromycota: A Review of Current Genetic Resources.

    PubMed

    De Fine Licht, H H; Hajek, A E; Eilenberg, J; Jensen, A B

    2016-01-01

    The order Entomophthorales, which formerly contained c.280 species, has recently been recognized as a separate phylum, Entomophthoromycota, consisting of three recognized classes and six families. Many genera in this group contain obligate insect-pathogenic species with narrow host ranges, capable of producing epizootics in natural insect populations. Available sequence information from the phylum Entomophthoromycota can be classified into three main categories: first, partial gene regions (exons+introns) used for phylogenetic inference; second, protein coding gene regions obtained using degenerate primers, expressed sequence tag methodology or de novo transcriptome sequencing with molecular function inferred by homology analysis; and third, primarily forthcoming whole-genome sequencing data sets. Here we summarize the current genetic resources for Entomophthoromycota and identify research areas that are likely to be significantly advanced from the availability of new whole-genome resources.

  20. Development and perspectives of scientific services offered by genomic biological resource centres.

    PubMed

    Wagner, Florian; Heidtke, Karsten R; Drescher, Bernd; Radelof, Uwe

    2007-09-01

    A number of fundamental technical developments like the evolvement of oligonucleotide microarrays, new sequencing technologies and gene synthesis have considerably changed the character of genomic biological resource centres in recent years. While genomic biological resource centres traditionally served mainly as providers of sparsely characterized cDNA clones and clone sets, there is nowadays a clear tendency towards well-characterized, high-quality clones. In addition, major new service units like microarray services have developed, which are completely independent of clone collections, reflecting the co-evolution of data generation and technology development. The new technologies require an increasingly higher degree of specialization, data integration and quality standards. Altogether, these developments result in spin-offs of highly specialized biotech companies, some of which will take a prominent position in translational medicine.

  1. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

    PubMed Central

    Wyffels, Jennifer; L. King, Benjamin; Vincent, James; Chen, Chuming; Wu, Cathy H.; Polson, Shawn W.

    2014-01-01

    Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase ( http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources. PMID:25309735

  2. StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

    PubMed

    Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

    2016-01-01

    The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

  3. StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

    PubMed

    Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

    2016-01-01

    The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my. PMID:27138013

  4. StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform

    PubMed Central

    Zheng, Wenning; Paterson, Ian C.; Mutha, Naresh V. R.; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A.; Jakubovics, Nicholas S.; Choo, Siew Woh

    2016-01-01

    The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my. PMID:27138013

  5. RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA.

    PubMed

    Chen, Lei; Ai, Peng; Zhang, Jinfeng; Deng, Qiming; Wang, Shiquan; Li, Shuangcheng; Zhu, Jun; Li, Ping; Zheng, Aiping

    2016-01-01

    Rice [Oryza sativa (L.)] feeds more than half of the world's population. Rhizoctonia solaniis a major fungal pathogen of rice causing extreme crop losses in all rice-growing regions of the world. R. solani AG1 IA is a major cause of sheath blight in rice. In this study, we constructed a comprehensive and user-friendly web-based database, RSIADB, to analyse its draft genome and transcriptome. The database was built using the genome sequence (10,489 genes) and annotation information for R. solani AG1 IA. A total of six RNAseq samples of R. solani AG1 IA were also analysed, corresponding to 10, 18, 24, 32, 48 and 72 h after infection of rice leaves. The RSIADB database enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, Sequence Extractor, Browse and Construction Diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource will facilitate studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection. Database URL:http://genedenovoweb.ticp.net:81/rsia/index.php.

  6. From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

    PubMed Central

    2011-01-01

    Background The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. Results More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. Conclusions The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye. PMID:21951788

  7. AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species

    PubMed Central

    Aurrecoechea, Cristina; Barreto, Ana; Brestelli, John; Brunk, Brian P.; Caler, Elisabet V.; Fischer, Steve; Gajria, Bindu; Gao, Xin; Gingle, Alan; Grant, Greg; Harb, Omar S.; Heiges, Mark; Iodice, John; Kissinger, Jessica C.; Kraemer, Eileen T.; Li, Wei; Nayak, Vishal; Pennington, Cary; Pinney, Deborah F.; Pitts, Brian; Roos, David S.; Srinivasamoorthy, Ganesh; Stoeckert, Christian J.; Treatman, Charles; Wang, Haiming

    2011-01-01

    AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB. Importantly they utilize the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user’s profile for future retrieval and may also be shared with other researchers using a unique strategy web address. PMID:20974635

  8. RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA

    PubMed Central

    Ai, Peng; Zhang, Jinfeng; Deng, Qiming; Wang, Shiquan; Li, Shuangcheng; Zhu, Jun; Li, Ping; Zheng, Aiping

    2016-01-01

    Rice [Oryza sativa (L.)] feeds more than half of the world’s population. Rhizoctonia solani is a major fungal pathogen of rice causing extreme crop losses in all rice-growing regions of the world. R. solani AG1 IA is a major cause of sheath blight in rice. In this study, we constructed a comprehensive and user-friendly web-based database, RSIADB, to analyse its draft genome and transcriptome. The database was built using the genome sequence (10 489 genes) and annotation information for R. solani AG1 IA. A total of six RNAseq samples of R. solani AG1 IA were also analysed, corresponding to 10, 18, 24, 32, 48 and 72 h after infection of rice leaves. The RSIADB database enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, Sequence Extractor, Browse and Construction Diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource will facilitate studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection. Database URL: http://genedenovoweb.ticp.net:81/rsia/index.php PMID:27022158

  9. RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA.

    PubMed

    Chen, Lei; Ai, Peng; Zhang, Jinfeng; Deng, Qiming; Wang, Shiquan; Li, Shuangcheng; Zhu, Jun; Li, Ping; Zheng, Aiping

    2016-01-01

    Rice [Oryza sativa (L.)] feeds more than half of the world's population. Rhizoctonia solaniis a major fungal pathogen of rice causing extreme crop losses in all rice-growing regions of the world. R. solani AG1 IA is a major cause of sheath blight in rice. In this study, we constructed a comprehensive and user-friendly web-based database, RSIADB, to analyse its draft genome and transcriptome. The database was built using the genome sequence (10,489 genes) and annotation information for R. solani AG1 IA. A total of six RNAseq samples of R. solani AG1 IA were also analysed, corresponding to 10, 18, 24, 32, 48 and 72 h after infection of rice leaves. The RSIADB database enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, Sequence Extractor, Browse and Construction Diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource will facilitate studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection. Database URL:http://genedenovoweb.ticp.net:81/rsia/index.php. PMID:27022158

  10. arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies

    PubMed Central

    Baudis, Michael

    2012-01-01

    Background The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing number of projects have mapped CNAs using high-resolution microarray based techniques. So far, no single resource does provide a global collection of readily accessible oncogenomic array data. Methodology/Principal Findings We here present arrayMap, a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. To date, the resource incorporates more than 40,000 arrays in 224 cancer types extracted from several resources, including the NCBI’s Gene Expression Omnibus (GEO), EBI’s ArrayExpress (AE), The Cancer Genome Atlas (TCGA), publication supplements and direct submissions. For the majority of the included datasets, probe level and integrated visualization facilitate gene level and genome wide data review. Results from multi-case selections can be connected to downstream data analysis and visualization tools. Conclusions/Significance To our knowledge, currently no data source provides an extensive collection of high resolution oncogenomic CNA data which readily could be used for genomic feature mining, across a representative range of cancer entities. arrayMap represents our effort for providing a long term platform for oncogenomic CNA data independent of specific platform considerations or specific project dependence. The online database can be accessed at http//www.arraymap.org. PMID:22629346

  11. Fuel bed characteristics of Sierra Nevada conifers

    USGS Publications Warehouse

    van Wagtendonk, J.W.; Benedict, J.M.; Sydoriak, W.M.

    1998-01-01

    A study of fuels in Sierra Nevada conifer forests showed that fuel bed depth and fuel bed weight significantly varied by tree species and developmental stage of the overstory. Specific values for depth and weight of woody, litter, and duff fuels are reported. There was a significant positive relationship between fuel bed depth and weight. Estimates of woody fuel weight using the planar intercept method were significantly related to sampled values. These relationships can be used to estimate fuel weights in the field.

  12. Computational methods and resources for the interpretation of genomic variants in cancer

    PubMed Central

    2015-01-01

    The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencing the whole exomes and or genomes of cancer patients in the thousands, thereby providing an invaluable collection of new somatic mutations in different cancer types. These initiatives promoted the development of methods and tools for the analysis of cancer genomes that are aimed at studying the relationship between genotype and phenotype in cancer. In this article we review the online resources and computational tools for the analysis of cancer genome. First, we describe the available repositories of cancer genome data. Next, we provide an overview of the methods for the detection of genetic variation and computational tools for the prioritization of cancer related genes and causative somatic variations. Finally, we discuss the future perspectives in cancer genomics focusing on the impact of computational methods and quantitative approaches for defining personalized strategies to improve the diagnosis and treatment of cancer. PMID:26111056

  13. Computational methods and resources for the interpretation of genomic variants in cancer.

    PubMed

    Tian, Rui; Basu, Malay K; Capriotti, Emidio

    2015-01-01

    The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencing the whole exomes and or genomes of cancer patients in the thousands, thereby providing an invaluable collection of new somatic mutations in different cancer types. These initiatives promoted the development of methods and tools for the analysis of cancer genomes that are aimed at studying the relationship between genotype and phenotype in cancer. In this article we review the online resources and computational tools for the analysis of cancer genome. First, we describe the available repositories of cancer genome data. Next, we provide an overview of the methods for the detection of genetic variation and computational tools for the prioritization of cancer related genes and causative somatic variations. Finally, we discuss the future perspectives in cancer genomics focusing on the impact of computational methods and quantitative approaches for defining personalized strategies to improve the diagnosis and treatment of cancer.

  14. flyDIVaS: A Comparative Genomics Resource for Drosophila Divergence and Selection

    PubMed Central

    Stanley, Craig E.; Kulathinal, Rob J.

    2016-01-01

    With arguably the best finished and expertly annotated genome assembly, Drosophila melanogaster is a formidable genetics model to study all aspects of biology. Nearly a decade ago, the 12 Drosophila genomes project expanded D. melanogaster’s breadth as a comparative model through the community-development of an unprecedented genus- and genome-wide comparative resource. However, since its inception, these datasets for evolutionary inference and biological discovery have become increasingly outdated, outmoded, and inaccessible. Here, we provide an updated and upgradable comparative genomics resource of Drosophila divergence and selection, flyDIVaS, based on the latest genomic assemblies, curated FlyBase annotations, and recent OrthoDB orthology calls. flyDIVaS is an online database containing D. melanogaster-centric orthologous gene sets, CDS and protein alignments, divergence statistics (% gaps, dN, dS, dN/dS), and codon-based tests of positive Darwinian selection. Out of 13,920 protein-coding D. melanogaster genes, ∼80% have one aligned ortholog in the closely related species, D. simulans, and ∼50% have 1–1 12-way alignments in the original 12 sequenced species that span over 80 million yr of divergence. Genes and their orthologs can be chosen from four different taxonomic datasets differing in phylogenetic depth and coverage density, and visualized via interactive alignments and phylogenetic trees. Users can also batch download entire comparative datasets. A functional survey finds conserved mitotic and neural genes, highly diverged immune and reproduction-related genes, more conspicuous signals of divergence across tissue-specific genes, and an enrichment of positive selection among highly diverged genes. flyDIVaS will be regularly updated and can be freely accessed at www.flydivas.info. We encourage researchers to regularly use this resource as a tool for biological inference and discovery, and in their classrooms to help train the next generation of

  15. NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

    PubMed Central

    Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

    2016-01-01

    Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

  16. NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

    PubMed

    Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

    2016-01-01

    Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

  17. NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

    PubMed

    Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

    2016-01-01

    Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

  18. The Culture Collection of Algae and Protozoa (CCAP): a biological resource for protistan genomics.

    PubMed

    Gachon, Claire M M; Day, John G; Campbell, Christine N; Pröschold, Thomas; Saxon, Rachel J; Küpper, Frithjof C

    2007-12-30

    CCAP, the largest European protistan culture collection, is based at the Scottish Association for Marine Science near Oban, Scotland (http://www.ccap.ac.uk). The Collection comprises more than 2700 strains in the public domain, of which 1050 are marine algae, 1300 freshwater algae, and 350 protozoa. The primary mission of CCAP is to maintain and distribute defined cultures and their associated information to its customers. It also has a support and advisory function on all aspects of protistan science. In addition, it is involved in the training of students and researchers in algal identification and culture techniques. In light of the increasing number of fully sequenced protists, the CCAP is striving to provide targeted services and support to workers involved in all aspects of genomic research. At present, the Collection holds several hundred strains of genomic model taxa including: Acanthamoeba, Cafeteria, Cercomonas, Chlamydomonas, Chlorella, Cyanophora, Dictyostelium, Dunaliella, Ectocarpus, Emiliania, Euglena, Micromonas, Naegleria, Nephroselmis, Paramecium, Pavlova, Phaeodactylum, Porphyra, Pseudendoclonium, Pylaiella, Rhodomonas, Scenedesmus, Staurastrum, Tetrahymena, Thalassiosira, Volvox and Zygnema. These strains provide a defined representation of natural variation within model organisms, an increasingly useful resource for post-genomics approaches. Our aim over the next 2-5 years is to add value to the Collection by increasing the number of genome model species, and by offering an integrated, up-to-date, easy-to-use resource that would provide curated information on our strain holdings. In collaboration with other major Biological Resource Centres worldwide, we intend to build a hub providing access to both protistan cultures and their associated bioinformatics data.

  19. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Crow, John [National Center for Genome Resources

    2016-07-12

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  20. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    Crow, John

    2012-06-01

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  1. Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome.

    PubMed

    Ralph, Steven G; Yueh, Hesther; Friedmann, Michael; Aeschliman, Dana; Zeznik, Jeffrey A; Nelson, Colleen C; Butterfield, Yaron S N; Kirkpatrick, Robert; Liu, Jerry; Jones, Steven J M; Marra, Marco A; Douglas, Carl J; Ritland, Kermit; Bohlmann, Jörg

    2006-08-01

    Conifers are resistant to attack from a large number of potential herbivores or pathogens. Previous molecular and biochemical characterization of selected conifer defence systems support a model of multigenic, constitutive and induced defences that act on invading insects via physical, chemical, biochemical or ecological (multitrophic) mechanisms. However, the genomic foundation of the complex defence and resistance mechanisms of conifers is largely unknown. As part of a genomics strategy to characterize inducible defences and possible resistance mechanisms of conifers against insect herbivory, we developed a cDNA microarray building upon a new spruce (Picea spp.) expressed sequence tag resource. This first-generation spruce cDNA microarray contains 9720 cDNA elements representing c. 5500 unique genes. We used this array to monitor gene expression in Sitka spruce (Picea sitchensis) bark in response to herbivory by white pine weevils (Pissodes strobi, Curculionidae) or wounding, and in young shoot tips in response to western spruce budworm (Choristoneura occidentalis, Lepidopterae) feeding. Weevils are stem-boring insects that feed on phloem, while budworms are foliage feeding larvae that consume needles and young shoot tips. Both insect species and wounding treatment caused substantial changes of the host plant transcriptome detected in each case by differential gene expression of several thousand array elements at 1 or 2 d after the onset of treatment. Overall, there was considerable overlap among differentially expressed gene sets from these three stress treatments. Functional classification of the induced transcripts revealed genes with roles in general plant defence, octadecanoid and ethylene signalling, transport, secondary metabolism, and transcriptional regulation. Several genes involved in primary metabolic processes such as photosynthesis were down-regulated upon insect feeding or wounding, fitting with the concept of dynamic resource allocation in plant

  2. Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses

    PubMed Central

    Crovadore, Julien; Cochard, Bastien; Calmin, Gautier; Chablais, Romain; Schulz, Torsten

    2016-01-01

    We report here the whole-genome shotgun sequences of the strain UASWS1009 of the species Mesorhizobium hungaricum sp. nov., which are different from any other known Mesorhizobium species. This is the first genome registered for this new species, which could be considered as a potential resource for agriculture and environmental uses. PMID:27738050

  3. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access t...

  4. Conifer expansion reduces the competitive ability and herbivore defense of aspen by modifying light environment and soil chemistry.

    PubMed

    Calder, W John; Horn, Kevin J; St Clair, Samuel B

    2011-06-01

    Disturbance patterns strongly influence plant community structure. What remains less clear, particularly at a mechanistic level, is how changes in disturbance cycles alter successional outcomes in plant communities. There is evidence that fire suppression is resulting in longer fire return intervals in subalpine forests and that these lengthened intervals increase competitive interactions between aspen and conifer species. We conducted a field and greenhouse study to compare photosynthesis, growth and defense responses of quaking aspen and subalpine fir regeneration under light reductions and shifts in soil chemistry that occur as conifers increase in dominance. The studies demonstrated that aspen regeneration was substantially more sensitive to light and soil resource limitations than that of subalpine fir. For aspen, light reductions and/or shifts in soil chemistry limited height growth, biomass gain, photosynthesis and the production of defense compounds (phenolic glycosides and condensed tannins). Biomass gain and phenolic glycoside concentrations were co-limited by light reduction and changes in soil chemistry. In contrast, subalpine fir seedlings tended to be more tolerant of low light conditions and showed no sensitivity to changes in soil chemistry. Unlike aspen, subalpine fir increased its root to shoot ratio on conifer soils, which may partially explain its maintenance of growth and defense. The results suggest that increasing dominance of conifers in subalpine forests alters light conditions and soil chemistry in a way that places greater physiological and growth constraints on aspen than subalpine fir, with a likely outcome being more successful recruitment of conifers and losses in aspen cover.

  5. Soybean Knowledge Base (SoyKB): a Web Resource for Soybean Translational Genomics

    SciTech Connect

    Joshi, Trupti; Patil, Kapil; Fitzpatrick, Michael R.; Franklin, Levi D.; Yao, Qiuming; Cook, Jeffrey R.; Wang, Zhem; Libault, Marc; Brechenmacher, Laurent; Valliyodan, Babu; Wu, Xiaolei; Cheng, Jianlin; Stacey, Gary; Nguyen, Henry T.; Xu, Dong

    2012-01-17

    Background: Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs). Methods: SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/ metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers of registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers. Conclusions: SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/.

  6. Resources

    MedlinePlus

    ... Breastfeeding - resources Bulimia - resources Burns - resources Cancer - resources Cerebral palsy - resources Celiac disease - resources Child abuse - resources Chronic fatigue syndrome - resources Chronic pain - ...

  7. NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes

    PubMed Central

    Geisen, Stefanie; Barturen, Guillermo; Alganza, Ángel M.; Hackenberg, Michael; Oliver, José L.

    2014-01-01

    The updated release of ‘NGSmethDB’ (http://bioinfo2.ugr.es/NGSmethDB) is a repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes. Short-read data sets from NGS bisulfite-sequencing projects of cell lines, fresh and pathological tissues are first pre-processed and aligned to the corresponding reference genome, and then the cytosine methylation levels are profiled. One major improvement is the application of a unique bioinformatics protocol to all data sets, thereby assuring the comparability of all values with each other. We implemented stringent quality controls to minimize important error sources, such as sequencing errors, bisulfite failures, clonal reads or single nucleotide variants (SNVs). This leads to reliable and high-quality methylomes, all obtained under uniform settings. Another significant improvement is the detection in parallel of SNVs, which might be crucial for many downstream analyses (e.g. SNVs and differential-methylation relationships). A next-generation methylation browser allows fast and smooth scrolling and zooming, thus speeding data download/upload, at the same time requiring fewer server resources. Several data mining tools allow the comparison/retrieval of methylation levels in different tissues or genome regions. NGSmethDB methylomes are also available as native tracks through a UCSC hub, which allows comparison with a wide range of third-party annotations, in particular phenotype or disease annotations. PMID:24271385

  8. The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond.

    PubMed

    Mueller, Lukas A; Solow, Teri H; Taylor, Nicolas; Skwarecki, Beth; Buels, Robert; Binns, John; Lin, Chenwei; Wright, Mark H; Ahrens, Robert; Wang, Ying; Herbst, Evan V; Keyder, Emil R; Menda, Naama; Zamir, Dani; Tanksley, Steven D

    2005-07-01

    The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond.

  9. The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1

    PubMed Central

    Mueller, Lukas A.; Solow, Teri H.; Taylor, Nicolas; Skwarecki, Beth; Buels, Robert; Binns, John; Lin, Chenwei; Wright, Mark H.; Ahrens, Robert; Wang, Ying; Herbst, Evan V.; Keyder, Emil R.; Menda, Naama; Zamir, Dani; Tanksley, Steven D.

    2005-01-01

    The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond. PMID:16010005

  10. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.

    PubMed

    Varshney, Rajeev K; Song, Chi; Saxena, Rachit K; Azam, Sarwar; Yu, Sheng; Sharpe, Andrew G; Cannon, Steven; Baek, Jongmin; Rosen, Benjamin D; Tar'an, Bunyamin; Millan, Teresa; Zhang, Xudong; Ramsay, Larissa D; Iwata, Aiko; Wang, Ying; Nelson, William; Farmer, Andrew D; Gaur, Pooran M; Soderlund, Carol; Penmetsa, R Varma; Xu, Chunyan; Bharti, Arvind K; He, Weiming; Winter, Peter; Zhao, Shancen; Hane, James K; Carrasquilla-Garcia, Noelia; Condie, Janet A; Upadhyaya, Hari D; Luo, Ming-Cheng; Thudi, Mahendar; Gowda, C L L; Singh, Narendra P; Lichtenzveig, Judith; Gali, Krishna K; Rubio, Josefa; Nadarajan, N; Dolezel, Jaroslav; Bansal, Kailash C; Xu, Xun; Edwards, David; Zhang, Gengyun; Kahl, Guenter; Gil, Juan; Singh, Karam B; Datta, Swapan K; Jackson, Scott A; Wang, Jun; Cook, Douglas R

    2013-03-01

    Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea--desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

  11. Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression

    PubMed Central

    Garcia-Vedrenne, Ana Elisa; Groner, Maya; Page-Karjian, Annie; Siegmund, Gregor-Fausto; Singhal, Sonia; Sziklay, Jamie; Roberts, Steven

    2013-01-01

    Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX). QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens. PMID:24069279

  12. GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

    PubMed Central

    Samson, Delphine; Legeai, Fabrice; Karsenty, Emmanuelle; Reboux, Sébastien; Veyrieras, Jean-Baptiste; Just, Jeremy; Barillot, Emmanuel

    2003-01-01

    Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/. PMID:12519976

  13. Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

    PubMed Central

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

  14. Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.

    PubMed

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology.

  15. Conifer health classification for Colorado, 2008

    USGS Publications Warehouse

    Cole, Christopher J.; Noble, Suzanne M.; Blauer, Steven L.; Friesen, Beverly A.; Curry, Stacy E.; Bauer, Mark A.

    2010-01-01

    Colorado has undergone substantial changes in forests due to urbanization, wildfires, insect-caused tree mortality, and other human and environmental factors. The U.S. Geological Survey Rocky Mountain Geographic Science Center evaluated and developed a methodology for applying remotely-sensed imagery for assessing conifer health in Colorado. Two classes were identified for the purposes of this study: healthy and unhealthy (for example, an area the size of a 30- x 30-m pixel with 20 percent or greater visibly dead trees was defined as ?unhealthy?). Medium-resolution Landsat 5 Thematic Mapper imagery were collected. The normalized, reflectance-converted, cloud-filled Landsat scenes were merged to form a statewide image mosaic, and a Normalized Difference Vegetation Index (NDVI) and Renormalized Difference Infrared Index (RDII) were derived. A supervised maximum likelihood classification was done using the Landsat multispectral bands, the NDVI, the RDII, and 30-m U.S. Geological Survey National Elevation Dataset (NED). The classification was constrained to pixels identified in the updated landcover dataset as coniferous or mixed coniferous/deciduous vegetation. The statewide results were merged with a separate health assessment of Grand County, Colo., produced in late 2008. Sampling and validation was done by collecting field data and high-resolution imagery. The 86 percent overall classification accuracy attained in this study suggests that the data and methods used successfully characterized conifer conditions within Colorado. Although forest conditions for Lodgepole Pine (Pinus contorta) are easily characterized, classification uncertainty exists between healthy/unhealthy Ponderosa Pine (Pinus ponderosa), Pi?on (Pinus edulis), and Juniper (Juniperus sp.) vegetation. Some underestimation of conifer mortality in Summit County is likely, where recent (2008) cloud-free imagery was unavailable. These classification uncertainties are primarily due to the spatial and

  16. Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon.

    PubMed

    Argyris, Jason M; Pujol, Marta; Martín-Hernández, Ana Montserrat; Garcia-Mas, Jordi

    2015-09-01

    The availability of the genome sequence of many crop species during the past few years has opened a new era in plant biology, allowing for the performance of massive genomic studies in plant species other than the classical models Arabidopsis and rice. One of these crop species is melon (Cucumis melo), a cucurbit of high economic value that has become an interesting model for the study of biological processes such as fruit ripening, sex determination and phloem transport. The recent availability of the melon genome sequence, together with a number of genetic and genomic resources, provides powerful tools that can be used to assist in the main melon breeding targets, namely disease resistance and fruit quality. In this review, we will describe recent data obtained combining the use of a melon near isogenic line (NIL) population and genomic resources to gain insight into agronomically important traits as fruit ripening, resistance to Cucumber Mosaic virus (CMV) and the accumulation of sugars in fruits.

  17. A genome-scale resource for the functional characterization of Arabidopsis transcription factors

    PubMed Central

    Pruneda-Paz, Jose L.; Breton, Ghislain; Nagel, Dawn H.; Kang, S. Earl; Bonaldi, Katia; Doherty, Colleen J.; Ravelo, Stephanie; Galli, Mary; Ecker, Joseph R.; Kay, Steve A.

    2014-01-01

    SUMMARY Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs) bound to gene promoters. TF-promoter interactions thus provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive clone-collection of Arabidopsis TFs created to provide a versatile resource to uncover TF biological functions. We leveraged this collection by implementing a high-throughput DNA-binding assay and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes. PMID:25043187

  18. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

    PubMed

    Harb, Omar S; Roos, David S

    2015-01-01

    Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

  19. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

    PubMed

    Harb, Omar S; Roos, David S

    2015-01-01

    Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods. PMID:25388105

  20. Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries

    PubMed Central

    Saski, Christopher A.; Bhattacharjee, Ranjana; Scheffler, Brian E.; Asiedu, Robert

    2015-01-01

    The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches

  1. Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries.

    PubMed

    Saski, Christopher A; Bhattacharjee, Ranjana; Scheffler, Brian E; Asiedu, Robert

    2015-01-01

    The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches

  2. Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries.

    PubMed

    Saski, Christopher A; Bhattacharjee, Ranjana; Scheffler, Brian E; Asiedu, Robert

    2015-01-01

    The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches

  3. Gondwanan conifer clones imperilled by bushfire

    PubMed Central

    Worth, James R. P.; Sakaguchi, Shota; Rann, Karl D.; Bowman, Clarence J. W.; Ito, Motomi; Jordan, Gregory J.; Bowman, David M. J. S.

    2016-01-01

    Global increases in fire frequency driven by anthropogenic greenhouse emissions and land use change could threaten unique and ancient species by creeping into long-term fire refugia. The perhumid and mountainous western half of Tasmania is a globally important refugium for palaeo-endemic, fire intolerant lineages, especially conifers. Reproductive strategy will be crucial to the resilience of these organisms under warmer, dryer and more fire prone climates. This study analysed clonal versus sexual reproduction in old growth plots dominated by the palaeo-endemic conifer Athrotaxis cupressoides (Cupressaceae), a species that lacks any traits to tolerate frequent landscape fire. Across most of the seven plots the amount of sexually derived individuals was lower than clonally derived with, on average, 60% of all stems belonging to the same multi-locus lineage (MLL) (i.e. were clonal). Some MLLs were large spanning over 10 s of metres and consisted of up to 62 stems. The high mortality after fire and the rarity of sexual regeneration means that the range of this fire-intolerant species is likely to contract under enhanced fire regimes and has a limited capacity to disperse via seed to available fire refugia in the landscape. PMID:27666536

  4. Plant hormones and ecophysiology of conifers

    SciTech Connect

    Davies, W.J.

    1995-07-01

    Over the past 30 years, there have been very substantial fluctuations in the interests of plant scientists in the involvement of plant growth regulators in the control of physiology, growth, and development of plants. In the years following the identification of the five major classes of growth regulators and identification of other groups of compounds of somewhat more restricted interest, an enormous number of papers reported the effects of hormones applied externally to a very wide range of plants. During this period, it became very fashionable to compare effects of hormones with the effects of the environment on developmental and physiological phenomena and to suggest a regulatory role for the hormone(s) in the processes under consideration. Ross et al. (1983) have published a very comprehensive survey of the effects of growth regulators applied externally to conifers, and even 10 years later, it is difficult to improve on what they have done. Nevertheless, in the light of recent changes in our understanding of how growth regulators may work, it is necessary to reexamine this field and ask what we really know about the involvement of growth regulators in the ecophysiology of conifers.

  5. Limited resources of genome sequencing in developing countries: Challenges and solutions.

    PubMed

    Helmy, Mohamed; Awad, Mohamed; Mosa, Kareem A

    2016-06-01

    The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classification systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN) and the World Bank (WB) systems. The UN classification system uses the UN Human Development Index (HDI), an indicator that uses statistic of life expectancy, education, and income per capita for countries' classification. While the WB system uses gross national income (GNI) per capita that is calculated using the World Bank Atlas method. According to the UN and WB classification systems, there are 151 and 134 developing countries, respectively, with 89% overlap between the two systems. Developing countries have limited human development, and limited expenditure in education and research, among several other limitations. The biggest challenge facing genomic researchers and clinicians is limited resources. As a result, genomic tools, specifically genome sequencing technologies, which are rapidly becoming indispensable, are not widely available. In this report, we explore the current status of sequencing technologies in developing countries, describe the associated challenges and emphasize potential solutions. PMID:27354935

  6. Limited resources of genome sequencing in developing countries: Challenges and solutions.

    PubMed

    Helmy, Mohamed; Awad, Mohamed; Mosa, Kareem A

    2016-06-01

    The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classification systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN) and the World Bank (WB) systems. The UN classification system uses the UN Human Development Index (HDI), an indicator that uses statistic of life expectancy, education, and income per capita for countries' classification. While the WB system uses gross national income (GNI) per capita that is calculated using the World Bank Atlas method. According to the UN and WB classification systems, there are 151 and 134 developing countries, respectively, with 89% overlap between the two systems. Developing countries have limited human development, and limited expenditure in education and research, among several other limitations. The biggest challenge facing genomic researchers and clinicians is limited resources. As a result, genomic tools, specifically genome sequencing technologies, which are rapidly becoming indispensable, are not widely available. In this report, we explore the current status of sequencing technologies in developing countries, describe the associated challenges and emphasize potential solutions.

  7. Exploiting Genomics Resources to Identify Candidate Genes Underlying Antioxidants Content in Tomato Fruit

    PubMed Central

    Calafiore, Roberta; Ruggieri, Valentino; Raiola, Assunta; Rigano, Maria M.; Sacco, Adriana; Hassan, Mohamed I.; Frusciante, Luigi; Barone, Amalia

    2016-01-01

    The tomato is a model species for fleshy fruit development and ripening, as well as for genomics studies of others Solanaceae. Many genetic and genomics resources, including databases for sequencing, transcriptomics and metabolomics data, have been developed and are today available. The purpose of the present work was to uncover new genes and/or alleles that determine ascorbic acid and carotenoids accumulation, by exploiting one Solanum pennellii introgression lines (IL7-3) harboring quantitative trait loci (QTL) that increase the content of these metabolites in the fruit. The higher ascorbic acid and carotenoids content in IL7-3 was confirmed at three fruit developmental stages. The tomato genome reference sequence and the recently released S. pennellii genome sequence were investigated to identify candidate genes (CGs) that might control ascorbic acid and carotenoids accumulation. First of all, a refinement of the wild region borders in the IL7-3 was achieved by analyzing CAPS markers designed in our laboratory. Afterward, six CGs associated to ascorbic acid and one with carotenoids metabolism were identified exploring the annotation and the Gene Ontology terms of genes included in the region. Variants between the sequence of the wild and the cultivated alleles of these genes were investigated for their functional relevance and their potential effects on the protein sequences were predicted. Transcriptional levels of CGs in the introgression region were extracted from RNA-Seq data available for the entire S. pennellii introgression lines collection and verified by Real-Time qPCR. Finally, seven IL7-3 sub-lines were genotyped using 28 species-specific markers and then were evaluated for metabolites content. These analyses evidenced a significant decrease in transcript abundance for one 9-cis-epoxycarotenoid dioxygenase and one L-ascorbate oxidase homolog, whose role in the accumulation of carotenoids and ascorbic acid is discussed. Comprehensively, the reported

  8. Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing

    PubMed Central

    Roberts, Steven B.; Hauser, Lorenz; Seeb, Lisa W.; Seeb, James E.

    2012-01-01

    Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis. PMID:22383979

  9. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

    PubMed

    Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

    2016-06-01

    MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

  10. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

    PubMed

    Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

    2016-06-01

    MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. PMID:26919060

  11. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

    PubMed

    Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

    2015-06-01

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. PMID:26133641

  12. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics

    PubMed Central

    Tzika, Athanasia C.; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C.

    2015-01-01

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the “Reptilian Transcriptomes Database 2.0,” which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. PMID:26133641

  13. AmeriFlux US-Vcm Valles Caldera Mixed Conifer

    SciTech Connect

    Litvak, Marcy

    2016-01-01

    This is the AmeriFlux version of the carbon flux data for the site US-Vcm Valles Caldera Mixed Conifer. Site Description - The Valles Caldera Mixed Conifer site is located in the 1200 km2 Jemez River basin in north-central New Mexico. Common to elevations ranging from 3040 to 2740 m in the region, the mixed conifer stand, within the entirety of the tower footprint in all directions, provides an excellent setting for studying the seasonal interaction between snow and vegetation.

  14. Conifer Decline and Mortality in Siberia

    NASA Astrophysics Data System (ADS)

    Kharuk, V.; Im, S.; Ranson, K.

    2015-12-01

    "Dark needle conifer" (DNC: Abies sibirica, Pinus sibirica and Picea obovata) decline and mortality increase were documented in Russia during recent decades. Here we analyzed causes and scale of Siberian pine and fir mortality in Altai-Sayan and Baikal Lake Regions and West Siberian Plane based on in situdata and remote sensing (QuickBird, Landsat, GRACE). Geographically, mortality began on the margins of the DNC range (i.e., within the forest-steppe and conifer-broadleaf ecotones) and on terrain features with maximal water stress risk (narrow-shaped hilltops, convex steep south facing slopes, shallow well-drained soils). Within ridges, mortality occurred mainly along mountain passes, where stands faced drying winds. Regularly mortality was observed to decrease with elevation increase with the exception of Baikal Lake Mountains, where it was minimal near the lake shore and increased with elevation (up to about 1000 m a.s.l.). Siberian pine and fir mortality followed a drying trend with consecutive droughts since the 1980s. Dendrochronology analysis showed that mortality was correlated with vapor pressure deficit increase, drought index, soil moisture decrease and occurrence of late frosts. In Baikal region Siberian pine mortality correlated with Baikal watershed meteorological variables. An impact of previous year climate conditions on the current growth was found (r2 = 0.6). Thus, water-stressed trees became sensitive to bark beetles and fungi impact (including Polygraphus proximus and Heterobasidion annosum). At present, an increase in mortality is observed within the majority of DNC range. Results obtained also showed a primary role of water stress in that phenomenon with a secondary role of bark beetles and fungi attacks. In future climate with increased drought severity and frequency Siberian pine and fir will partly disappear from its current range, and will be substituted by drought-tolerant species (e.g., Pinus silvestris, Larix sibirica).

  15. The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species.

    PubMed

    Childs, Kevin L; Konganti, Kranti; Buell, C Robin

    2012-01-01

    Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources. Database URL: http://bfgr.plantbiology.msu.edu.

  16. Open access resources for genome-wide association mapping in rice.

    PubMed

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  17. Open access resources for genome-wide association mapping in rice

    PubMed Central

    McCouch, Susan R.; Wright, Mark H.; Tung, Chih-Wei; Maron, Lyza G.; McNally, Kenneth L.; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J.; Naredo, Ma. Elizabeth B.; Mercado, Sheila Mae Q.; Harrington, Sandra E.; Shi, Yuxin; Branchini, Darcy A.; Kuser-Falcão, Paula R.; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  18. Open access resources for genome-wide association mapping in rice.

    PubMed

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

  19. A genome-wide resource for the analysis of protein localisation in Drosophila

    PubMed Central

    Sarov, Mihail; Barz, Christiane; Jambor, Helena; Hein, Marco Y; Schmied, Christopher; Suchold, Dana; Stender, Bettina; Janosch, Stephan; KJ, Vinay Vikas; Krishnan, RT; Krishnamoorthy, Aishwarya; Ferreira, Irene RS; Ejsmont, Radoslaw K; Finkl, Katja; Hasse, Susanne; Kämpfer, Philipp; Plewka, Nicole; Vinis, Elisabeth; Schloissnig, Siegfried; Knust, Elisabeth; Hartenstein, Volker; Mann, Matthias; Ramaswami, Mani; VijayRaghavan, K; Tomancak, Pavel; Schnorrer, Frank

    2016-01-01

    The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts. DOI: http://dx.doi.org/10.7554/eLife.12068.001 PMID:26896675

  20. Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.

    PubMed

    Enault, François; Suhre, Karsten; Poirot, Olivier; Abergel, Chantal; Claverie, Jean-Michel

    2003-07-01

    Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.

  1. Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design

    PubMed Central

    Ramsey, John S; Wilson, Alex CC; de Vos, Martin; Sun, Qi; Tamborindeguy, Cecilia; Winfield, Agnese; Malloch, Gaynor; Smith, Dawn M; Fenton, Brian; Gray, Stewart M; Jander, Georg

    2007-01-01

    Background The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. Results Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. Conclusion New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible interactions with its

  2. The Earliest Evidence of Holometabolan Insect Pupation in Conifer Wood

    PubMed Central

    Tapanila, Leif; Roberts, Eric M.

    2012-01-01

    Background The pre-Jurassic record of terrestrial wood borings is poorly resolved, despite body fossil evidence of insect diversification among xylophilic clades starting in the late Paleozoic. Detailed analysis of borings in petrified wood provides direct evidence of wood utilization by invertebrate animals, which typically comprises feeding behaviors. Methodology/Principal Findings We describe a U-shaped boring in petrified wood from the Late Triassic Chinle Formation of southern Utah that demonstrates a strong linkage between insect ontogeny and conifer wood resources. Xylokrypta durossi new ichnogenus and ichnospecies is a large excavation in wood that is backfilled with partially digested xylem, creating a secluded chamber. The tracemaker exited the chamber by way of a small vertical shaft. This sequence of behaviors is most consistent with the entrance of a larva followed by pupal quiescence and adult emergence — hallmarks of holometabolous insect ontogeny. Among the known body fossil record of Triassic insects, cupedid beetles (Coleoptera: Archostemata) are deemed the most plausible tracemakers of Xylokrypta, based on their body size and modern xylobiotic lifestyle. Conclusions/Significance This oldest record of pupation in fossil wood provides an alternative interpretation to borings once regarded as evidence for Triassic bees. Instead Xylokrypta suggests that early archostematan beetles were leaders in exploiting wood substrates well before modern clades of xylophages arose in the late Mesozoic. PMID:22355387

  3. Novel genomic resources for a climate change sensitive mammal: characterization of the American pika transcriptome

    PubMed Central

    2013-01-01

    Background When faced with climate change, species must either shift their home range or adapt in situ in order to maintain optimal physiological balance with their environment. The American pika (Ochotona princeps) is a small alpine mammal with limited dispersal capacity and low tolerance for thermal stress. As a result, pikas have become an important system for examining biotic responses to changing climatic conditions. Previous research using amplified fragment length polymorphisms (AFLPs) has revealed evidence for environmental-mediated selection in O. princeps populations distributed along elevation gradients, yet the anonymity of AFLP loci and lack of available genomic resources precluded the identification of associated gene regions. Here, we harnessed next-generation sequencing technology in order to characterize the American pika transcriptome and identify a large suite of single nucleotide polymorphisms (SNPs), which can be used to elucidate elevation- and site-specific patterns of sequence variation. Results We constructed pooled cDNA libraries of O. princeps from high (1400m) and low (300m) elevation sites along a previously established transect in British Columbia. Transcriptome sequencing using the Roche 454 GS FLX titanium platform generated 780 million base pairs of data, which were assembled into 7,325 high coverage contigs. These contigs were used to identify 24,261 novel SNP loci. Using high resolution melt analysis, we developed 17 of these SNPs into genotyping assays, which were validated with independent DNA samples from British Columbia Canada and Oregon State USA. In addition, we detected haplotypes in the NADH dehydrogenase subunit 5 of the mitochondrial genome that were fixed and different among elevations, suggesting that this may be an informative target gene for studying the role of cellular respiration in local adaptation. We also identified contigs that were unique to each elevation, including a high elevation-specific contig that was

  4. Aberrant Classopollis pollen reveals evidence for unreduced (2n) pollen in the conifer family Cheirolepidiaceae during the Triassic-Jurassic transition.

    PubMed

    Kürschner, Wolfram M; Batenburg, Sietske J; Mander, Luke

    2013-10-01

    Polyploidy (or whole-genome doubling) is a key mechanism for plant speciation leading to new evolutionary lineages. Several lines of evidence show that most species among flowering plants had polyploidy ancestry, but it is virtually unknown for conifers. Here, we study variability in pollen tetrad morphology and the size of the conifer pollen type Classopollis extracted from sediments of the Triassic-Jurassic transition, 200 Ma. Classopollis producing Cheirolepidiaceae were one of the most dominant and diverse groups of conifers during the Mesozoic. We show that aberrant pollen Classopollis tetrads, triads and dyads, and the large variation in pollen size indicates the presence of unreduced (2n) pollen, which is one of the main mechanisms in modern polyploid formation. Polyploid speciation may explain the high variability of growth forms and adaptation of these conifers to different environments and their resistance to extreme growth conditions. We suggest that polyploidy may have also reduced the extinction risk of these conifers during the End-Triassic biotic crisis.

  5. Aberrant Classopollis pollen reveals evidence for unreduced (2n) pollen in the conifer family Cheirolepidiaceae during the Triassic–Jurassic transition

    PubMed Central

    Kürschner, Wolfram M.; Batenburg, Sietske J.; Mander, Luke

    2013-01-01

    Polyploidy (or whole-genome doubling) is a key mechanism for plant speciation leading to new evolutionary lineages. Several lines of evidence show that most species among flowering plants had polyploidy ancestry, but it is virtually unknown for conifers. Here, we study variability in pollen tetrad morphology and the size of the conifer pollen type Classopollis extracted from sediments of the Triassic–Jurassic transition, 200 Ma. Classopollis producing Cheirolepidiaceae were one of the most dominant and diverse groups of conifers during the Mesozoic. We show that aberrant pollen Classopollis tetrads, triads and dyads, and the large variation in pollen size indicates the presence of unreduced (2n) pollen, which is one of the main mechanisms in modern polyploid formation. Polyploid speciation may explain the high variability of growth forms and adaptation of these conifers to different environments and their resistance to extreme growth conditions. We suggest that polyploidy may have also reduced the extinction risk of these conifers during the End-Triassic biotic crisis. PMID:23926159

  6. High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

    PubMed Central

    2013-01-01

    Background Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation. Results Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix. Conclusions The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes. PMID:23924375

  7. Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.

    PubMed

    Hodgins, Kathryn A; Yeaman, Sam; Nurkowski, Kristin A; Rieseberg, Loren H; Aitken, Sally N

    2016-06-01

    The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers. PMID:26873578

  8. GenomicusPlants: A Web Resource to Study Genome Evolution in Flowering Plants

    PubMed Central

    Louis, Alexandra; Murat, Florent; Salse, Jérôme; Roest Crollius, Hugues

    2015-01-01

    Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces (‘views’) are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes ‘painted’ with colours of another genome of interest. All four views are interconnected and benefit from many customizable features. PMID:25432975

  9. GenomicusPlants: a web resource to study genome evolution in flowering plants.

    PubMed

    Louis, Alexandra; Murat, Florent; Salse, Jérôme; Crollius, Hugues Roest

    2015-01-01

    Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces ('views') are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes 'painted' with colours of another genome of interest. All four views are interconnected and benefit from many customizable features.

  10. RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

    PubMed Central

    2013-01-01

    Background Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). Description RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. Conclusions RegPrecise 3.0 gives access to the

  11. Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus).

    PubMed

    Lea, Amanda J; Altmann, Jeanne; Alberts, Susan C; Tung, Jenny

    2016-04-01

    Variation in resource availability commonly exerts strong effects on fitness-related traits in wild animals. However, we know little about the molecular mechanisms that mediate these effects, or about their persistence over time. To address these questions, we profiled genome-wide whole-blood DNA methylation levels in two sets of wild baboons: (i) 'wild-feeding' baboons that foraged naturally in a savanna environment and (ii) 'Lodge' baboons that had ready access to spatially concentrated human food scraps, resulting in high feeding efficiency and low daily travel distances. We identified 1014 sites (0.20% of sites tested) that were differentially methylated between wild-feeding and Lodge baboons, providing the first evidence that resource availability shapes the epigenome in a wild mammal. Differentially methylated sites tended to occur in contiguous stretches (i.e., in differentially methylated regions or DMRs), in promoters and enhancers, and near metabolism-related genes, supporting their functional importance in gene regulation. In agreement, reporter assay experiments confirmed that methylation at the largest identified DMR, located in the promoter of a key glycolysis-related gene, was sufficient to causally drive changes in gene expression. Intriguingly, all dispersing males carried a consistent epigenetic signature of their membership in a wild-feeding group, regardless of whether males dispersed into or out of this group as adults. Together, our findings support a role for DNA methylation in mediating ecological effects on phenotypic traits in the wild and emphasize the dynamic environmental sensitivity of DNA methylation levels across the life course.

  12. De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia.

    PubMed

    Singh, Rakesh; Kumar, Rajesh; Mahato, Ajay Kumar; Paliwal, Ritu; Singh, Amit Kumar; Kumar, Sundeep; Marla, Soma S; Kumar, Ashok; Singh, Nagendra K

    2016-09-01

    Tinospora cordifolia is known for its medicinal properties owing to the presence of useful constituents such as terpenes, glycosides, steroids, alkaloids, and flavonoids belonging to secondary metabolism origin. However, there is little information available pertaining to critical genomic elements (ESTs, molecular markers) necessary for judicious exploitation of its germplasm. We employed 454 GS-FLX pyrosequencing of entire transcripts and altogether ∼25 K assembled transcripts or Expressed sequence tags (ESTs) were identified. As the interest in T. cordifolia is primarily due to its secondary metabolite constituents, the ESTs pertaining to terpenoids biosynthetic pathway were identified in the present study. Additionally, several ESTs were assigned to different transcription factor families. To validate our transcripts dataset, the novel EST-SSR markers were generated to assess the genetic diversity among germplasm of T. cordifolia. These EST-SSR markers were found to be polymorphic and the dendrogram based on dice similarity index revealed three distinct clustering of accessions. The present study demonstrates effectiveness in using both NEWBLER and MIRA sequence read assembler software for enriching transcript-dataset and thus enables better exploitation of EST resources for mining candidate genes and designing molecular markers. PMID:27465295

  13. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology.

    PubMed

    Abaan, Ogan D; Polley, Eric C; Davis, Sean R; Zhu, Yuelin J; Bilke, Sven; Walker, Robert L; Pineda, Marbin; Gindin, Yevgeniy; Jiang, Yuan; Reinhold, William C; Holbeck, Susan L; Simon, Richard M; Doroshow, James H; Pommier, Yves; Meltzer, Paul S

    2013-07-15

    The NCI-60 cell lines are the most frequently studied human tumor cell lines in cancer research. This panel has generated the most extensive cancer pharmacology database worldwide. In addition, these cell lines have been intensely investigated, providing a unique platform for hypothesis-driven research focused on enhancing our understanding of tumor biology. Here, we report a comprehensive analysis of coding variants in the NCI-60 panel of cell lines identified by whole exome sequencing, providing a list of possible cancer specific variants for the community. Furthermore, we identify pharmacogenomic correlations between specific variants in genes such as TP53, BRAF, ERBBs, and ATAD5 and anticancer agents such as nutlin, vemurafenib, erlotinib, and bleomycin showing one of many ways the data could be used to validate and generate novel hypotheses for further investigation. As new cancer genes are identified through large-scale sequencing studies, the data presented here for the NCI-60 will be an invaluable resource for identifying cell lines with mutations in such genes for hypothesis-driven research. To enhance the utility of the data for the greater research community, the genomic variants are freely available in different formats and from multiple sources including the CellMiner and Ingenuity websites. PMID:23856246

  14. Databases of genomic variation and phenotypes: existing resources and future needs

    PubMed Central

    Johnston, Jennifer J.; Biesecker, Leslie G.

    2013-01-01

    Massively parallel sequencing (MPS) has become an important tool for identifying medically significant variants in both research and the clinic. Accurate variation and genotype–phenotype databases are critical in our ability to make sense of the vast amount of information that MPS generates. The purpose of this review is to summarize the state of the art of variation and genotype–phenotype databases, how they can be used, and opportunities to improve these resources. Our working assumption is that the objective of the clinical genomicist is to identify highly penetrant variants that could explain existing disease or predict disease risk for individual patients or research participants. We have detailed how current databases contribute to this goal providing frequency data, literature reviews and predictions of causation for individual variants. For variant annotation, databases vary greatly in their ease of use, the use of standard mutation nomenclature, the comprehensiveness of the variant cataloging and the degree of expert opinion. Ultimately, we need a dynamic and comprehensive reference database of medically important variants that is easily cross referenced to exome and genome sequence data and allows for an accumulation of expert opinion. PMID:23962721

  15. Causes and consequences of variation in conifer leaf life-span

    SciTech Connect

    Reich, P.B.; Koike, T.; Gower, S.T.; Schoettle, A.W.

    1995-07-01

    Species with mutually supporting traits, such as high N{sub mass}, SLA, and A{sub mass}, and short leaf life-span, tend to inhabit either generally resource-rich environments or spatial and/or temporal microhabitats that are resource-rich in otherwise more limited habitats (e.g., {open_quotes}precipitation{close_quotes} ephemerals in warm deserts or spring ephemerals in the understory of temperate deciduous forests). In contrast, species with long leaf life-span often support foliage with low SLA, N{sub mass}, and A{sub mass}, and often grow in low-temperature limited, dry, and/or nutrient-poor environments. The contrast between evergreen and deciduous species, and the implications that emerge from such comparisons, can be considered a paradigm of modern ecological theory. However, based on the results of Reich et al. (1992) and Gower et al. (1993), coniferous species with foliage that persists for 9-10 years are likely to assimilate and allocate carbon and nutrients differently than other evergreen conifers that retain foliage for 2-3 years. Thus, attempts to contrast ecophysiological or ecosystem characteristics of evergreen versus deciduous life forms may be misleading, and pronounced differences among evergreen conifers may be ignored. Clearly, the deciduous-evergreen contrast, although useful in several ways, should be viewed from the broader perspective of a gradient in leaf life-span.

  16. Role of quinate dehydrogenase in quinic acid metabolism in conifers

    SciTech Connect

    Osipov, V.I.; Shein, I.V.

    1986-08-10

    Quinate dehydrogenase was isolated from young needles of the Siberian larch and partially purified by ammonium sulfate fractionation. It was found that in conifers, in contrast to other plants, quinate dehydrogenase is active both with NAD and with NADP. The values of K/sub m/ for quinate and NADP were 1.8 and 0.18 mM. The enzyme exhibits maximum activity at pH 9.0. It was assumed that NADP-dependent quinate dehydrogenase is responsible for quinic acid synthesis. The special features of the organization and regulation of the initial stages of the shikimate pathway in conifers are discussed.

  17. Wildlife species associated with non-coniferous vegetation in Pacific Northwest conifer forests: A review

    USGS Publications Warehouse

    Hagar, J.C.

    2007-01-01

    Non-coniferous vegetation, including herbs, shrubs, and broad-leaved trees, makes a vital contribution to ecosystem function and diversity in Pacific Northwest conifer forests. However, forest management has largely been indifferent or detrimental to shrubs and trees that have low commercial value, in spite of a paradigm shift towards more holistic management in recent decades. Forest management practices that are detrimental to broad-leaved trees and shrubs are likely to decrease habitat diversity for wildlife, but the number of species that may be affected has not previously been enumerated. I reviewed life history accounts for forest-dwelling vertebrate wildlife species and derived a list of 78 species in Oregon and Washington that are associated with non-coniferous vegetation. The diversity of direct and indirect food resources provided was the primary functional basis for associations of most species with non-coniferous vegetation. Thus, a diversity of herbs and broad-leaved trees and shrubs provides the foundation for food webs that contribute to diversity at multiple trophic levels in Pacific Northwest conifer forests. Given the number of species associated with non-coniferous vegetation in conifer-dominated forests, maintaining habitats that support diverse plant communities, particularly broad-leaved trees and shrubs, will be an important component of management strategies intended to foster biodiversity. Silvicultural practices such as modified planting densities, and pre-commercial and commercial thinning, can be used to control stand density in order to favor the development of understory herbs, shrubs, and a diversity of tree species within managed stands. Allowing shrubs and hardwood trees to develop and persist in early seral stands by curtailing vegetation control also would benefit many species associated with non-coniferous vegetation.

  18. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

    PubMed Central

    Scannell, Devin R.; Zill, Oliver A.; Rokas, Antonis; Payen, Celia; Dunham, Maitreya J.; Eisen, Michael B.; Rine, Jasper; Johnston, Mark; Hittinger, Chris Todd

    2011-01-01

    High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental and evolutionary research. We present improved genome sequences of three species of Saccharomyces sensu stricto yeasts: S. bayanus var. uvarum (CBS 7001), S. kudriavzevii (IFO 1802T and ZP 591), and S. mikatae (IFO 1815T), and describe their comparison to the genomes of S. cerevisiae and S. paradoxus. The new sequences, derived by assembling millions of short DNA sequence reads together with previously published Sanger shotgun reads, have vastly greater long-range continuity and far fewer gaps than the previously available genome sequences. New gene predictions defined a set of 5261 protein-coding orthologs across the five most commonly studied Saccharomyces yeasts, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses. To facilitate experimental investigations, we generated genetically marked, stable haploid strains for all three of these Saccharomyces species. These nearly complete genome sequences and the collection of genetically marked strains provide a valuable toolset for comparative studies of gene function, metabolism, and evolution, and render Saccharomyces sensu stricto the most experimentally tractable model genus. These resources are freely available and accessible through www.SaccharomycesSensuStricto.org. PMID:22384314

  19. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

    PubMed Central

    Aurrecoechea, Cristina; Brestelli, John; Carlton, Jane M.; Dommer, Jennifer; Fischer, Steve; Gajria, Bindu; Gao, Xin; Gingle, Alan; Harb, Omar S.; Heiges, Mark; Innamorato, Frank; Iodice, John; Kissinger, Jessica C.; Kraemer, Eileen; Li, Wei; Miller, John A.; Morrison, Hilary G.; Nayak, Vishal; Pennington, Cary; Pinney, Deborah F.; Roos, David S.; Ross, Chris; Sullivan, Steven; Treatman, Charles; Wang, Haiming

    2009-01-01

    GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data. PMID:18824479

  20. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.

    PubMed

    Aurrecoechea, Cristina; Brestelli, John; Brunk, Brian P; Carlton, Jane M; Dommer, Jennifer; Fischer, Steve; Gajria, Bindu; Gao, Xin; Gingle, Alan; Grant, Greg; Harb, Omar S; Heiges, Mark; Innamorato, Frank; Iodice, John; Kissinger, Jessica C; Kraemer, Eileen; Li, Wei; Miller, John A; Morrison, Hilary G; Nayak, Vishal; Pennington, Cary; Pinney, Deborah F; Roos, David S; Ross, Chris; Stoeckert, Christian J; Sullivan, Steven; Treatman, Charles; Wang, Haiming

    2009-01-01

    GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data. PMID:18824479

  1. FveGD: an online resource for diploid strawberry (fragaria vesca) genomics data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system that is an emerging model for the Rosaceae family. An ancestral F. vesca genome contributed to the genome of the octoploid dessert strawberry (F. xananassa) and...

  2. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

    PubMed Central

    2014-01-01

    Background A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described. Results Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons. Conclusion Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles. PMID:24734980

  3. A Simple Computer Application for the Identification of Conifer Genera

    ERIC Educational Resources Information Center

    Strain, Steven R.; Chmielewski, Jerry G.

    2010-01-01

    The National Science Education Standards prescribe that an understanding of the importance of classifying organisms be one component of a student's educational experience in the life sciences. The use of a classification scheme to identify organisms is one way of addressing this goal. We describe Conifer ID, a computer application that assists…

  4. Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation.

    PubMed

    Detrich, H W; Amemiya, Chris T

    2010-12-01

    The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20 pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66-1.83 pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168 kb. Paired BAC-end reads representing ∼0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones).

  5. Antarctic Notothenioid Fishes: Genomic Resources and Strategies for Analyzing an Adaptive Radiation

    PubMed Central

    Detrich, H. W.; Amemiya, Chris T.

    2010-01-01

    The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20 pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66–1.83 pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168 kb. Paired BAC-end reads representing ∼0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones). PMID:21082069

  6. Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China

    PubMed Central

    Wang, Ting; Wang, Zhen; Xia, Fan; Su, Yingjuan

    2016-01-01

    Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies. PMID:27113970

  7. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot.

    PubMed

    Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andrés; Álvarez-Dios, José Antonio; Cabaleiro, Santiago; Caamaño, Rubén; Martínez, Paulino; Bouza, Carmen

    2016-01-01

    Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species. PMID:26901189

  8. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

    PubMed Central

    Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andrés; Álvarez-Dios, José Antonio; Cabaleiro, Santiago; Caamaño, Rubén; Martínez, Paulino; Bouza, Carmen

    2016-01-01

    Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species. PMID:26901189

  9. Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource

    PubMed Central

    Devailly, Guillaume; Mantsoki, Anna; Michoel, Tom; Joshi, Anagha

    2015-01-01

    Genome-wide data is accumulating in an unprecedented way in the public domain. Re-mining this data shows great potential to generate novel hypotheses. However this approach is dependent on the quality (technical and biological) of the underlying data. Here we performed a systematic analysis of chromatin immunoprecipitation (ChIP) sequencing data of transcription and epigenetic factors from the encyclopaedia of DNA elements (ENCODE) resource to demonstrate that about one third of conditions with replicates show low concordance between replicate peak lists. This serves as a case study to demonstrate a caveat concerning genome-wide analyses and highlights a need to validate the quality of each sample before performing further associative analyses. PMID:26619763

  10. Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica.

    PubMed

    Wu, Guo-Zhang; Shi, Qiu-Ming; Niu, Ya; Xing, Mei-Qing; Xue, Hong-Wei

    2008-01-01

    The Shanghai RAPESEED Database (RAPESEED, http://rapeseed.plantsignal.cn/) was created to provide the solid platform for functional genomics studies of oilseed crops with the emphasis on seed development and fatty acid metabolism. The RAPESEED includes the resource of 8462 unique ESTs, of which 3526 clones are with full length cDNA; the expression profiles of 8095 genes and the Serial Analysis of Gene Expression (SAGE, 23,895 unique tags) and tag-to-gene data during seed development. In addition, a total of approximately 14,700 M3 mutant populations were generated by ethylmethanesulfonate (EMS) mutagenesis and related seed quality information was determined using the Foss NIR System. Further, the TILLING (Targeting Induced Local Lesions IN Genomes) platform was established based on the generated EMS mutant population. The relevant information was collected in RAPESEED database, which can be searched through keywords, nucleotide or protein sequences, or seed quality parameters, and downloaded.

  11. Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

    PubMed Central

    2010-01-01

    Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space. PMID:21167071

  12. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

    PubMed

    Perry, George H; Reeves, Darryl; Melsted, Páll; Ratan, Aakrosh; Miller, Webb; Michelini, Katelyn; Louis, Edward E; Pritchard, Jonathan K; Mason, Christopher E; Gilad, Yoav

    2012-01-01

    We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ~2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ~10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage-a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.

  13. A Genome Sequence Resource for the Aye-Aye (Daubentonia madagascariensis), a Nocturnal Lemur from Madagascar

    PubMed Central

    Perry, George H.; Reeves, Darryl; Melsted, Páll; Ratan, Aakrosh; Miller, Webb; Michelini, Katelyn; Louis, Edward E.; Pritchard, Jonathan K.; Mason, Christopher E.; Gilad, Yoav

    2012-01-01

    We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ∼3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ∼2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ∼10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage—a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests. PMID:22155688

  14. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

    PubMed

    Perry, George H; Reeves, Darryl; Melsted, Páll; Ratan, Aakrosh; Miller, Webb; Michelini, Katelyn; Louis, Edward E; Pritchard, Jonathan K; Mason, Christopher E; Gilad, Yoav

    2012-01-01

    We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ~2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ~10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage-a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests. PMID:22155688

  15. Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data.

    PubMed

    Nigam, Rajni; Laulederkind, Stanley J F; Hayman, G Thomas; Smith, Jennifer R; Wang, Shur-Jen; Lowry, Timothy F; Petri, Victoria; De Pons, Jeff; Tutaj, Marek; Liu, Weisong; Jayaraman, Pushkala; Munzenmaier, Diane H; Worthey, Elizabeth A; Dwinell, Melinda R; Shimoyama, Mary; Jacob, Howard J

    2013-09-16

    The rat has been widely used as a disease model in a laboratory setting, resulting in an abundance of genetic and phenotype data from a wide variety of studies. These data can be found at the Rat Genome Database (RGD, http://rgd.mcw.edu/), which provides a platform for researchers interested in linking genomic variations to phenotypes. Quantitative trait loci (QTLs) form one of the earliest and core datasets, allowing researchers to identify loci harboring genes associated with disease. These QTLs are not only important for those using the rat to identify genes and regions associated with disease, but also for cross-organism analyses of syntenic regions on the mouse and the human genomes to identify potential regions for study in these organisms. Currently, RGD has data on >1,900 rat QTLs that include details about the methods and animals used to determine the respective QTL along with the genomic positions and markers that define the region. RGD also curates human QTLs (>1,900) and houses>4,000 mouse QTLs (imported from Mouse Genome Informatics). Multiple ontologies are used to standardize traits, phenotypes, diseases, and experimental methods to facilitate queries, analyses, and cross-organism comparisons. QTLs are visualized in tools such as GBrowse and GViewer, with additional tools for analysis of gene sets within QTL regions. The QTL data at RGD provide valuable information for the study of mapped phenotypes and identification of candidate genes for disease associations.

  16. A sea urchin genome project: sequence scan, virtual map, and additional resources.

    PubMed

    Cameron, R A; Mahairas, G; Rast, J P; Martinez, P; Biondi, T R; Swartzell, S; Wallace, J C; Poustka, A J; Livingston, B T; Wray, G A; Ettensohn, C A; Lehrach, H; Britten, R J; Davidson, E H; Hood, L

    2000-08-15

    Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 125 kb). The BAC-end sequence tag connectors (STCs) occur an average of 10 kb apart, and, together with restriction digest patterns recorded for the same BAC clones, they provide immediate access to contigs of several hundred kilobases surrounding any gene of interest. The STCs survey >5% of the genome and provide the estimate that this genome contains approximately 27,350 protein-coding genes. The frequency distribution and canonical sequences of all middle and highly repetitive sequence families in the genome were obtained from the STCs as well. The 500-kb Hox gene complex of this species is being sequenced in its entirety. In addition, arrayed cDNA libraries of >10(5) clones each were constructed from every major stage of embryogenesis, several individual cell types, and adult tissues and are available to the community. The accumulated STC data and an expanding expressed sequence tag database (at present including >12, 000 sequences) have been reported to GenBank and are accessible on public web sites.

  17. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products.

    PubMed

    Geisler, Katrin; Jensen, Niels Berg; Yuen, Macaire M S; Madilao, Lina; Bohlmann, Jörg

    2016-05-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes. PMID:26936895

  18. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products.

    PubMed

    Geisler, Katrin; Jensen, Niels Berg; Yuen, Macaire M S; Madilao, Lina; Bohlmann, Jörg

    2016-05-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes.

  19. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products1[OPEN

    PubMed Central

    Yuen, Macaire M.S.; Bohlmann, Jörg

    2016-01-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I–IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes. PMID:26936895

  20. Analysis of conifer forest regeneration using Landsat Thematic Mapper data

    NASA Technical Reports Server (NTRS)

    Fiorella, Maria; Ripple, William J.

    1995-01-01

    Landsat Thematic Mapper (TM) data were used to evaluate young conifer stands in the western Cascade Mountains of Oregon. Regression and correlation analyses were used to describe the relationships between TM band values and age of young Douglas-fir stands (2 to 35 years old). Spectral data from well regenerated Douglas-fir stands were compared to those of poorly regenerated conifer stands. TM bands 1, 2, 3, 5, 6, and 7 were inversely correlated with the age (r greater than or equal to -0.80) of well regenerated Douglas-fir stands. Overall, the 'structural index' (TM 4/5 ratio) had the highest correlation to age of Douglas-fir stands (r = 0.96). Poorly regenerated stands were spectrally distinct from well regenerated Douglas-fir stands after the stands reached an age of approximately 15 years.

  1. Development of a D genome specific marker resource for diploid and hexaploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those of the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of po...

  2. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.

    PubMed

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates. PMID:27633273

  3. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chickpea (Cicer arietinum) is the world’s second most important grain legume crop, accounting for a significant proportion of human dietary protein and playing a critical role in food security in developing countries. We report the sequence of the ~738 Mb kabuli (CDC Frontier) chickpea genome, which...

  4. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Consequently, comprehensive databases of variation among thousands of varieties is currently being assembled and released. Proper analysi...

  5. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.

    PubMed

    Varshney, Rajeev K; Chen, Wenbin; Li, Yupeng; Bharti, Arvind K; Saxena, Rachit K; Schlueter, Jessica A; Donoghue, Mark T A; Azam, Sarwar; Fan, Guangyi; Whaley, Adam M; Farmer, Andrew D; Sheridan, Jaime; Iwata, Aiko; Tuteja, Reetu; Penmetsa, R Varma; Wu, Wei; Upadhyaya, Hari D; Yang, Shiaw-Pyng; Shah, Trushar; Saxena, K B; Michael, Todd; McCombie, W Richard; Yang, Bicheng; Zhang, Gengyun; Yang, Huanming; Wang, Jun; Spillane, Charles; Cook, Douglas R; May, Gregory D; Xu, Xun; Jackson, Scott A

    2012-01-01

    Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries. PMID:22057054

  6. The MiST2 database: a comprehensive genomics resource on microbial signal transduction

    PubMed Central

    Ulrich, Luke E.; Zhulin, Igor B.

    2010-01-01

    The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%). PMID:19900966

  7. Black raspberry genomic and genetic resource development to enable cultivar improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This project incorporates use of phenotypic, genotypic and genomic data to advance and streamline identification of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis L.). A lack of adapted, disease resistant cultivars has...

  8. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

    PubMed Central

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md. Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates. PMID:27633273

  9. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis.

    PubMed

    Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha; Dhanda, Sandeep Kumar; Sehgal, Manika; Khan, Md Shoaib; Monga, Isha; Dar, Showkat Ahmad; Singh, Sandeep; Nagpal, Gandharva; Usmani, Salman Sadullah; Thakur, Anamika; Kaur, Gazaldeep; Sharma, Shivangi; Bhardwaj, Aman; Qureshi, Abid; Raghava, Gajendra Pal Singh; Kumar, Manoj

    2016-01-01

    Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (http://bioinfo.imtech.res.in/manojk/zikavr/), dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content. Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, codon context, usage bias and phylogenetic inferences at whole genome and proteome level with user-friendly visual environment. Further, glycosylation sites and molecular diagnostic primers were also analyzed. Most importantly, we also proposed potential therapeutically imperative constituents namely vaccine epitopes, siRNAs, miRNAs, sgRNAs and repurposing drug candidates.

  10. OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis.

    PubMed

    Whiteside, Matthew D; Winsor, Geoffrey L; Laird, Matthew R; Brinkman, Fiona S L

    2013-01-01

    Prediction of orthologs (homologous genes that diverged because of speciation) is an integral component of many comparative genomics methods. Although orthologs are more likely to have similar function versus paralogs (genes that diverged because of duplication), recent studies have shown that their degree of functional conservation is variable. Also, there are inherent problems with several large-scale ortholog prediction approaches. To address these issues, we previously developed Ortholuge, which uses phylogenetic distance ratios to provide more precise ortholog assessments for a set of predicted orthologs. However, the original version of Ortholuge required manual intervention and was not easily accessible; therefore, we now report the development of OrtholugeDB, available online at http://www.pathogenomics.sfu.ca/ortholugedb. OrtholugeDB provides ortholog predictions for completely sequenced bacterial and archaeal genomes from NCBI based on reciprocal best Basic Local Alignment Search Tool hits, supplemented with further evaluation by the more precise Ortholuge method. The OrtholugeDB web interface facilitates user-friendly and flexible ortholog analysis, from single genes to genomes, plus flexible data download options. We compare Ortholuge with similar methods, showing how it may more consistently identify orthologs with conserved features across a wide range of taxonomic distances. OrtholugeDB facilitates rapid, and more accurate, bacterial and archaeal comparative genomic analysis and large-scale ortholog predictions.

  11. Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist

    SciTech Connect

    Yin, Tongming; ZHANG, Dr. XINYE; Gunter, Lee E; Li, Shuxian; Wullschleger, Stan D; Huang, Prof. Minren; Tuskan, Gerald A

    2009-01-01

    In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.

  12. Low-frequency creep in CoNiFe films.

    NASA Technical Reports Server (NTRS)

    Bartran, D. S.; Bourne, H. C., Jr.; Chow, L. G.

    1972-01-01

    Domain wall motion excited by slow rise-time, bipolar, hard-axis pulses in vacuum deposited CoNiFe films from 1500 to 2000 A thick is studied. The results are consistent with those of comparable NiFe films. Furthermore, the wall coercivity is found to be the most significant sample property correlated to the low-frequency creep properties of all the samples.

  13. MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes.

    PubMed

    Mudunuri, Suresh B; Patnana, Sujan; Nagarajaram, Hampapathalu A

    2014-01-01

    The MICdb is a comprehensive relational database of perfect microsatellites extracted from completely sequenced and annotated genomes of bacteria and archaea. The current version MICdb3.0 is an updated and revised version of MICdb2.0. As compared with the previous version MICdb2.0, the current release is significantly improved in terms of much larger coverage of genomes, improved presentation of queried results, user-friendly administration module to manage Simple Sequence Repeat (SSR) data such as addition of new genomes, deletion of obsolete data, etc., and also removal of certain features deemed to be redundant. The new web-interface to the database called Microsatellite Analysis Server (MICAS) version 3.0 has been improved by the addition of powerful high-quality visualization tools to view the query results in the form of pie charts and bar graphs. All the query results and graphs can be exported in different formats so that the users can use them for further analysis. MICAS3.0 is also equipped with a unique genome comparison module using which users can do pair-wise comparison of genomes with regard to their microsatellite distribution. The advanced search module can be used to filter the repeats based on certain criteria such as filtering repeats of a particular motif/repeat size, extracting repeats of coding/non-coding regions, sort repeats, etc. The MICdb database has, therefore, been made portable to be administered by a person with the necessary administrative privileges. The MICdb3.0 database and analysis server can be accessed for free from www.cdfd.org.in/micas. Database URL: http://www.cdfd.org.in/micas.

  14. L-Band Radiometer Measurements of Conifer Forests

    NASA Technical Reports Server (NTRS)

    Lang, R.; LeVine, D.; Chauhan, N.; deMatthaeis, P.; Bidwell, S.; Haken, M.

    2000-01-01

    Airborne radiometer measurements have been made at L-band over conifer forests in Virginia to study radiometric response to biomass and soil moisture. The horizontally polarized synthetic aperture radiometer, ESTAR, has been deployed abroad a NASA-P3 aircraft which is based at the Goddard Space Flight Center's Wallops Flight Facility. The instrument has been mounted in the bomb bay of the P-3 and images data in the cross track direction. Aircraft and surface measurements were made in July, August and November of 1999 over relatively homogeneous conifer stands of varying biomass. The surface measurements included soil moisture measurements in several stands. The soil moisture was low during the July flight and highest in November after heavy rains had occurred. The microwave images clearly distinguished between the different forest stands. Stand age, obtained from International Paper Corporation which owns the stands, showed a strong correlation between brightness temperature and stand age. This agrees with previous simulation studies of conifer forests which show that the brightness temperature increases with increasing stand biomass. Research is continuing to seek a quantitative correlation between the observed brightness temperature of the stands and their biomass and surface soil moisture.

  15. The versatile worm: genetic and genomic resources for Caenorhabditis elegans research.

    PubMed

    Antoshechkin, Igor; Sternberg, Paul W

    2007-07-01

    Since its establishment as a model organism, Caenorhabditis elegans has been an invaluable tool for biological research. An immense spectrum of questions can be addressed using this small nematode, making it one of the most versatile and exciting model organisms. Although the many tools and resources developed by the C. elegans community greatly facilitate new discoveries, they can also overwhelm newcomers to the field. This Review aims to familiarize new worm researchers with the main resources, and help them to select the tools that are best suited for their needs. We also hope that it will be helpful in identifying new research opportunities and will promote the development of additional resources.

  16. The Maize Genetics and Genomics Database. The Community Resource for Access to Diverse Maize Data1

    PubMed Central

    Lawrence, Carolyn J.; Seigfried, Trent E.; Brendel, Volker

    2005-01-01

    The Maize Genetics and Genomics Database (MaizeGDB) serves the maize (Zea mays) research community by making a wealth of genetics and genomics data available through an intuitive Web-based interface. The goals of the MaizeGDB project are 3-fold: to provide a central repository for public maize information; to present the data through the MaizeGDB Web site in a way that recapitulates biological relationships; and to provide an array of computational tools that address biological questions in an easy-to-use manner at the site. In addition to these primary tasks, MaizeGDB team members also serve the community of maize geneticists by lending technical support for community activities, including the annual Maize Genetics Conference and various workshops, teaching researchers to use both the MaizeGDB Web site and Community Curation Tools, and engaging in collaboration with individual research groups to make their unique data types available through MaizeGDB. PMID:15888678

  17. PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation.

    PubMed

    Preston, Mark D; Assefa, Samuel A; Ocholla, Harold; Sutherland, Colin J; Borrmann, Steffen; Nzila, Alexis; Michon, Pascal; Hien, Tran Tinh; Bousema, Teun; Drakeley, Christopher J; Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A; Doumbo, Ogobara K; Nosten, Francois; Fairhurst, Rick M; Conway, David J; Roper, Cally; Clark, Taane G

    2014-06-01

    Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600,000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania). PMID:24338354

  18. PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation

    PubMed Central

    Preston, Mark D.; Assefa, Samuel A.; Ocholla, Harold; Sutherland, Colin J.; Borrmann, Steffen; Nzila, Alexis; Michon, Pascal; Hien, Tran Tinh; Bousema, Teun; Drakeley, Christopher J.; Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A.; Doumbo, Ogobara K.; Nosten, Francois; Fairhurst, Rick M.; Conway, David J.; Roper, Cally; Clark, Taane G.

    2014-01-01

    Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600 000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania). PMID:24338354

  19. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

    PubMed

    Yoshida, Catherine E; Kruczkiewicz, Peter; Laing, Chad R; Lingohr, Erika J; Gannon, Victor P J; Nash, John H E; Taboada, Eduardo N

    2016-01-01

    For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub

  20. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

    SciTech Connect

    Simon, M. I.; Kim, U.-J.

    2002-02-26

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.

  1. Genome-wide association study of porcine hematological parameters in a Large White × Minzhu F2 resource population.

    PubMed

    Luo, Weizhen; Chen, Shaokang; Cheng, Duxue; Wang, Ligang; Li, Yong; Ma, Xiaojun; Song, Xin; Liu, Xin; Li, Wen; Liang, Jing; Yan, Hua; Zhao, Kebin; Wang, Chuduan; Wang, Lixian; Zhang, Longchao

    2012-01-01

    Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of animals such as pigs. QTLs for hematological parameters (hematological traits) have been detected in pig chromosomes, although these are often mapped by linkage analysis to large intervals making identification of the underlying mutation problematic. Single nucleotide polymorphisms (SNPs) are the common form of genetic variation among individuals and are thought to account for the majority of inherited traits. In this study, a genome-wide association study (GWAS) was performed to detect regions of association with hematological traits in a three-generation resource population produced by intercrossing Large White boars and Minzhu sows during the period from 2007 to 2011. Illumina PorcineSNP60 BeadChip technology was used to genotype each animal and seven hematological parameters were measured (hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC) and red blood cell volume distribution width (RDW)). Data were analyzed in a three step Genome-wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) method. A total of 62 genome-wide significant and three chromosome-wide significant SNPs associated with hematological parameters were detected in this GWAS. Seven and five SNPs were associated with HCT and HGB, respectively. These SNPs were all located within the region of 34.6-36.5 Mb on SSC7. Four SNPs within the region of 43.7-47.0 Mb and fifty-five SNPs within the region of 42.2-73.8 Mb on SSC8 showed significant association with MCH and MCV, respectively. At chromosome-wide significant level, one SNP at 29.2 Mb on SSC1

  2. dbDNV: a resource of duplicated gene nucleotide variants in human genome.

    PubMed

    Ho, Meng-Ru; Tsai, Kuo-Wang; Chen, Chun-houh; Lin, Wen-chang

    2011-01-01

    Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified >10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1,236,956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while ∼58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases.

  3. Toward meaningful snag-management guidelines for postfire salvage logging in North American conifer forests.

    PubMed

    Hutto, Richard L

    2006-08-01

    The bird species in western North America that are most restricted to, and therefore most dependent on, severely burned conifer forests during the first years following afire event depend heavily on the abundant standing snags for perch sites, nest sites, and food resources. Thus, it is critical to develop and apply appropriate snag-management guidelines to implement postfire timber harvest operations in the same locations. Unfortunately, existing guidelines designed for green-tree forests cannot be applied to postfire salvage sales because the snag needs of snag-dependent species in burned forests are not at all similar to the snag needs of snag-dependent species in green-tree forests. Birds in burned forests have very different snag-retention needs from those cavity-nesting bird species that have served as the focus for the development of existing snag-management guidelines. Specifically, many postfire specialists use standing dead trees not only for nesting purposes but for feeding purposes as well. Woodpeckers, in particular specialize on wood-boring beetle larvae that are superabundant in fire-killed trees for several years following severe fire. Species such as the Black-backed Woodpecker (Picoides arcticus) are nearly restricted in their habitat distribution to severely burned forests. Moreover existing postfire salvage-logging studies reveal that most postfire specialist species are completely absent from burned forests that have been (even partially) salvage logged. I call for the long-overdue development and use of more meaningful snag-retention guidelines for postfire specialists, and I note that the biology of the most fire-dependent bird species suggests that even a cursory attempt to meet their snag needs would preclude postfire salvage logging in those severely burned conifer forests wherein the maintenance of biological diversity is deemed important.

  4. GeneSpeed Beta Cell: An Online Genomics Data Repository and Analysis Resource Tailored for the Islet Cell Biologist

    PubMed Central

    Quayum, Nayeem; Kutchma, Alecksandr; Sarkar, Suparna A.; Juhl, Kirstine; Gradwohl, Gerard; Mellitzer, Georg; Hutton, John C.; Jensen, Jan

    2008-01-01

    Objective. We here describe the development of a freely available online database resource, GeneSpeed Beta Cell, which has been created for the pancreatic islet and pancreatic developmental biology investigator community. Research Design and Methods. We have developed GeneSpeed Beta Cell as a separate component of the GeneSpeed database, providing a genomics-type data repository of pancreas and islet-relevant datasets interlinked with the domain-oriented GeneSpeed database. Results. GeneSpeed Beta Cell allows the query of multiple published and unpublished select genomics datasets in a simultaneous fashion (multiexperiment viewing) and is capable of defining intersection results from precomputed analysis of such datasets (multidimensional querying). Combined with the protein-domain categorization/assembly toolbox provided by the GeneSpeed database, the user is able to define spatial expression constraints of select gene lists in a relatively rigid fashion within the pancreatic expression space. We provide several demonstration case studies of relevance to islet cell biology and development of the pancreas that provide novel insight into islet biology. Conclusions. The combination of an exhaustive domain-based compilation of the transcriptome with gene array data of interest to the islet biologist affords novel methods for multidimensional querying between individual datasets in a rapid fashion, presently not available elsewhere. PMID:18795106

  5. Ensembl genomes 2016: more genomes, more complexity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

  6. The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome

    PubMed Central

    Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui; Mezheritsky, Yarik; Muller, Robert; Strait, Emily; Huala, Eva

    2015-01-01

    The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR’s biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR’s focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally-based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible. PMID:26201819

  7. Tipping point of a conifer forest ecosystem under severe drought

    NASA Astrophysics Data System (ADS)

    Huang, Kaicheng; Yi, Chuixiang; Wu, Donghai; Zhou, Tao; Zhao, Xiang; Blanford, William J.; Wei, Suhua; Wu, Hao; Ling, Du; Li, Zheng

    2015-02-01

    Drought-induced tree mortality has recently received considerable attention. Questions have arisen over the necessary intensity and duration thresholds of droughts that are sufficient to trigger rapid forest declines. The values of such tipping points leading to forest declines due to drought are presently unknown. In this study, we have evaluated the potential relationship between the level of tree growth and concurrent drought conditions with data of the tree growth-related ring width index (RWI) of the two dominant conifer species (Pinus edulis and Pinus ponderosa) in the Southwestern United States (SWUS) and the meteorological drought-related standardized precipitation evapotranspiration index (SPEI). In this effort, we determined the binned averages of RWI and the 11 month SPEI within the month of July within each bin of 30 of RWI in the range of 0-3000. We found a significant correlation between the binned averages of RWI and SPEI at the regional-scale under dryer conditions. The tipping point of forest declines to drought is predicted by the regression model as SPEItp = -1.64 and RWItp = 0, that is, persistence of the water deficit (11 month) with intensity of -1.64 leading to negligible growth for the conifer species. When climate conditions are wetter, the correlation between the binned averages of RWI and SPEI is weaker which we believe is most likely due to soil water and atmospheric moisture levels no longer being the dominant factor limiting tree growth. We also illustrate a potential application of the derived tipping point (SPEItp = -1.64) through an examination of the 2002 extreme drought event in the SWUS conifer forest regions. Distinguished differences in remote-sensing based NDVI anomalies were found between the two regions partitioned by the derived tipping point.

  8. Simulated and empiric wind pollination patterns of conifer ovulate cones

    PubMed Central

    Niklas, Karl J.

    1982-01-01

    Wind tunnel analyses of conifer ovulate cones indicate that the total geometry of the cone enhances the probability of pollen entrapment. Aerodynamic characteristics of cone scale-bract complexes are such that suspended pollen is directed toward the micropyles of attached ovules. Within the taxa examined, there appears to be a preferential entrapment by ovulate cones of pollen of the same species. The data are interpreted as evidence for an aerodynamic reciprocity between wind-suspended pollen and the structure of ovulate cones which increases the frequency of pollination and the potential for fertilization. Images PMID:16593147

  9. Bioactive Secondary Metabolites Produced by the Fungal Endophytes of Conifers.

    PubMed

    Stierle, Andrea A; Stierle, Donald B

    2015-10-01

    This is a review of bioactive secondary metabolites isolated from conifer-associated endophytic fungi from 1990-2014. This includes compounds with antimicrobial, anti-inflammatory, anti-proliferative and cytotoxic activity towards human cancer cell lines, and activity against either plant pathogens or plant insect pests. Compounds that were originally reported without associated activity were included if other studies ascribed activity to these compounds. Compounds were not included if they were exclusively phytotoxic or if they were isolated from active extracts but were not determined to be the active component of that extract. PMID:26669101

  10. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution.

    PubMed

    Goron, Travis L; Raizada, Manish N

    2015-01-01

    Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.

  11. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

    PubMed Central

    Goron, Travis L.; Raizada, Manish N.

    2015-01-01

    Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed “orphan cereals.” Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa. PMID:25852710

  12. A gene expression resource generated by genome-wide lacZ profiling in the mouse

    PubMed Central

    Tuck, Elizabeth; Estabel, Jeanne; Oellrich, Anika; Maguire, Anna Karin; Adissu, Hibret A.; Souter, Luke; Siragher, Emma; Lillistone, Charlotte; Green, Angela L.; Wardle-Jones, Hannah; Carragher, Damian M.; Karp, Natasha A.; Smedley, Damian; Adams, Niels C.; Bussell, James N.; Adams, David J.; Ramírez-Solis, Ramiro; Steel, Karen P.; Galli, Antonella; White, Jacqueline K.

    2015-01-01

    ABSTRACT Knowledge of the expression profile of a gene is a critical piece of information required to build an understanding of the normal and essential functions of that gene and any role it may play in the development or progression of disease. High-throughput, large-scale efforts are on-going internationally to characterise reporter-tagged knockout mouse lines. As part of that effort, we report an open access adult mouse expression resource, in which the expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter gene. Many specific and informative expression patterns were noted. Expression was most commonly observed in the testis and brain and was most restricted in white adipose tissue and mammary gland. Over half of the assessed genes presented with an absent or localised expression pattern (categorised as 0-10 positive structures). A link between complexity of expression profile and viability of homozygous null animals was observed; inactivation of genes expressed in ≥21 structures was more likely to result in reduced viability by postnatal day 14 compared with more restricted expression profiles. For validation purposes, this mouse expression resource was compared with Bgee, a federated composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Furthermore, there were 1207 observations of expression of a particular gene in an anatomical structure where Bgee had no data, indicating a large amount of novelty in our data set. Examples of expression data corroborating and extending genotype-phenotype associations and supporting disease gene candidacy are presented to demonstrate the potential of this powerful resource. PMID:26398943

  13. Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes

    PubMed Central

    Abe, Kiyomi; Ichikawa, Hiroaki

    2016-01-01

    Identification and elucidation of functions of plant genes is valuable for both basic and applied research. In addition to natural variation in model plants, numerous loss-of-function resources have been produced by mutagenesis with chemicals, irradiation, or insertions of transposable elements or T-DNA. However, we may be unable to observe loss-of-function phenotypes for genes with functionally redundant homologs and for those essential for growth and development. To offset such disadvantages, gain-of-function transgenic resources have been exploited. Activation-tagged lines have been generated using obligatory overexpression of endogenous genes by random insertion of an enhancer. Recent progress in DNA sequencing technology and bioinformatics has enabled the preparation of genomewide collections of full-length cDNAs (fl-cDNAs) in some model species. Using the fl-cDNA clones, a novel gain-of-function strategy, Fl-cDNA OvereXpressor gene (FOX)-hunting system, has been developed. A mutant phenotype in a FOX line can be directly attributed to the overexpressed fl-cDNA. Investigating a large population of FOX lines could reveal important genes conferring favorable phenotypes for crop breeding. Alternatively, a unique loss-of-function approach Chimeric REpressor gene Silencing Technology (CRES-T) has been developed. In CRES-T, overexpression of a chimeric repressor, composed of the coding sequence of a transcription factor (TF) and short peptide designated as the repression domain, could interfere with the action of endogenous TF in plants. Although plant TFs usually consist of gene families, CRES-T is effective, in principle, even for the TFs with functional redundancy. In this review, we focus on the current status of the gene-overexpression strategies and resources for identifying and elucidating novel functions of cereal genes. We discuss the potential of these research tools for identifying useful genes and phenotypes for application in crop breeding. PMID

  14. Genomic resources and genetic diversity of captive lesser kudu (Tragelaphus imberbis).

    PubMed

    Bock, Friederike; Gallus, Susanne; Janke, Axel; Hailer, Frank; Steck, Beatrice L; Kumar, Vikas; Nilsson, Maria A

    2014-01-01

    The lesser kudu (Tragelaphus imberbis) is a spiral-horned antelope native to northeastern Africa. Individuals kept in zoological gardens are suspected to be highly inbred due to few founder individuals and a small breeding stock. A morphological study suggested two distinct subspecies of the lesser kudu. However, subspecies designation and population structure in zoological gardens has not been analyzed using molecular markers. We analyzed one mitochondrial marker and two nuclear intron loci (total: 2,239 nucleotides) in 52 lesser kudu individuals. Of these, 48 individuals were bred in captivity and sampled from seven different zoos. The four remaining individuals were recently captured in Somalia and are currently held in the Maktoum zoo. Maternally inherited mitochondrial sequences indicate substantial amounts of genetic variation in the zoo populations, while the biparentally inherited intron sequences are, as expected, less variable. The analyzed individuals show 10 mitochondrial haplotypes with a maximal distance of 10 mutational steps. No prominent subspecies structure is detectable in this study. For further studies of the lesser kudu population genetics, we present microsatellite markers from a low-coverage genome survey using 454 sequencing technology. PMID:25043251

  15. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

    PubMed Central

    Gallego Romero, Irene; Pavlovic, Bryan J; Hernando-Herraez, Irene; Zhou, Xiang; Ward, Michelle C; Banovich, Nicholas E; Kagan, Courtney L; Burnett, Jonathan E; Huang, Constance H; Mitrano, Amy; Chavarria, Claudia I; Friedrich Ben-Nun, Inbar; Li, Yingchun; Sabatini, Karen; Leonardo, Trevor R; Parast, Mana; Marques-Bonet, Tomas; Laurent, Louise C; Loring, Jeanne F; Gilad, Yoav

    2015-01-01

    Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude. DOI: http://dx.doi.org/10.7554/eLife.07103.001 PMID:26102527

  16. Genomic resources and genetic diversity of captive lesser kudu (Tragelaphus imberbis).

    PubMed

    Bock, Friederike; Gallus, Susanne; Janke, Axel; Hailer, Frank; Steck, Beatrice L; Kumar, Vikas; Nilsson, Maria A

    2014-01-01

    The lesser kudu (Tragelaphus imberbis) is a spiral-horned antelope native to northeastern Africa. Individuals kept in zoological gardens are suspected to be highly inbred due to few founder individuals and a small breeding stock. A morphological study suggested two distinct subspecies of the lesser kudu. However, subspecies designation and population structure in zoological gardens has not been analyzed using molecular markers. We analyzed one mitochondrial marker and two nuclear intron loci (total: 2,239 nucleotides) in 52 lesser kudu individuals. Of these, 48 individuals were bred in captivity and sampled from seven different zoos. The four remaining individuals were recently captured in Somalia and are currently held in the Maktoum zoo. Maternally inherited mitochondrial sequences indicate substantial amounts of genetic variation in the zoo populations, while the biparentally inherited intron sequences are, as expected, less variable. The analyzed individuals show 10 mitochondrial haplotypes with a maximal distance of 10 mutational steps. No prominent subspecies structure is detectable in this study. For further studies of the lesser kudu population genetics, we present microsatellite markers from a low-coverage genome survey using 454 sequencing technology.

  17. Explaining the distribution of breeding and dispersal syndromes in conifers.

    PubMed

    Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Donoghue, Michael J

    2013-11-01

    The evolution of plants exhibiting different sexes, or dioecy, is correlated with a number of ecological and life-history traits such as woody growth form and animal-dispersed seeds, but the underlying causes of these associations are unclear. Previous work in seed plants has suggested that the evolution of fleshy cones or seeds may favour dioecy. In this study, we use a well-sampled molecular phylogeny of conifers to show that although dioecy and fleshiness strongly co-occur at the species level, this relationship has not resulted from numerous separate origins of this trait combination or from differential rates of diversification. Instead, we suggest that two character combinations-the ancestral dry-monoecious condition and the derived fleshy-dioecious condition-have persisted in conifers longer than other combinations over evolutionary time. The persistence of these trait combinations appears to reflect differences in the rate of successful transition into and out of these character states over time, as well as the geographical restriction of species with rare combinations and their consequent vulnerability to extinction. In general, we argue that such persistence explanations should be considered alongside 'key innovation' hypotheses in explaining the phylogenetic distribution of traits.

  18. Integration and macroevolutionary patterns in the pollination biology of conifers.

    PubMed

    Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

    2015-06-01

    Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology.

  19. Explaining the distribution of breeding and dispersal syndromes in conifers

    PubMed Central

    Leslie, Andrew B.; Beaulieu, Jeremy M.; Crane, Peter R.; Donoghue, Michael J.

    2013-01-01

    The evolution of plants exhibiting different sexes, or dioecy, is correlated with a number of ecological and life-history traits such as woody growth form and animal-dispersed seeds, but the underlying causes of these associations are unclear. Previous work in seed plants has suggested that the evolution of fleshy cones or seeds may favour dioecy. In this study, we use a well-sampled molecular phylogeny of conifers to show that although dioecy and fleshiness strongly co-occur at the species level, this relationship has not resulted from numerous separate origins of this trait combination or from differential rates of diversification. Instead, we suggest that two character combinations—the ancestral dry-monoecious condition and the derived fleshy-dioecious condition—have persisted in conifers longer than other combinations over evolutionary time. The persistence of these trait combinations appears to reflect differences in the rate of successful transition into and out of these character states over time, as well as the geographical restriction of species with rare combinations and their consequent vulnerability to extinction. In general, we argue that such persistence explanations should be considered alongside ‘key innovation’ hypotheses in explaining the phylogenetic distribution of traits. PMID:24026822

  20. Corrosion properties of electroplated CoNiFe films

    SciTech Connect

    Saito, M.; Yamada, K.; Ohashi, K.; Yasue, Y.; Sogawa, Y.; Osaka, T.

    1999-08-01

    Electroplated CoNiFe films with a saturation flux density as high as 2.1 T are potentially useful in high-density magnetic recording heads. The authors found that films electroplated at a high current density (15 mA/cm{sup 2}) from a bath without saccharin have a sufficient anodic pitting-corrosion potential ({minus}65 mV). The authors also found that the pitting-corrosion potential of films electroplated under a low current density (5 mA/cm{sup 2}) from saccharin-free baths have anodic pitting-corrosion potentials of less than {minus}300 mV. However, the corrosion resistance improved after annealing at temperatures above 100 C. The crystal-grain boundaries in the as-plated film that electroplated under a low current density from saccharin-free baths are not clear (i.e., that the phase is amorphous). But the crystal grain boundaries in the annealed film are clear. Films electroplated from baths containing saccharin also have anodic pitting-corrosion potentials of less than {minus}300 mV. Their corrosion resistance did not improve when they were annealed at 250 C. The deterioration of the corrosion resistance is attributed to the defects that increase the face-centered cubic (111) lattice constant. One of the most important characteristics of a highly corrosion-resistant CoNiFe film is fine crystal structure with very few defects.

  1. Kinetics of tracheid development explain conifer tree-ring structure.

    PubMed

    Cuny, Henri E; Rathgeber, Cyrille B K; Frank, David; Fonti, Patrick; Fournier, Meriem

    2014-09-01

    Conifer tree rings are generally composed of large, thin-walled cells of light earlywood followed by narrow, thick-walled cells of dense latewood. Yet, how wood formation processes and the associated kinetics create this typical pattern remains poorly understood. We monitored tree-ring formation weekly over 3 yr in 45 trees of three conifer species in France. Data were used to model cell development kinetics, and to attribute the relative importance of the duration and rate of cell enlargement and cell wall deposition on tree-ring structure. Cell enlargement duration contributed to 75% of changes in cell diameter along the tree rings. Remarkably, the amount of wall material per cell was quite constant along the rings. Consequently, and in contrast with widespread belief, changes in cell wall thickness were not principally attributed to the duration and rate of wall deposition (33%), but rather to the changes in cell size (67%). Cell enlargement duration, as the main driver of cell size and wall thickness, contributed to 56% of wood density variation along the rings. This mechanistic framework now forms the basis for unraveling how environmental stresses trigger deviations (e.g. false rings) from the normal tree-ring structure.

  2. The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics.

    PubMed

    Huang, Ruili; Southall, Noel; Wang, Yuhong; Yasgar, Adam; Shinn, Paul; Jadhav, Ajit; Nguyen, Dac-Trung; Austin, Christopher P

    2011-04-27

    Small-molecule compounds approved for use as drugs may be "repurposed" for new indications and studied to determine the mechanisms of their beneficial and adverse effects. A comprehensive collection of all small-molecule drugs approved for human use would be invaluable for systematic repurposing across human diseases, particularly for rare and neglected diseases, for which the cost and time required for development of a new chemical entity are often prohibitive. Previous efforts to build such a comprehensive collection have been limited by the complexities, redundancies, and semantic inconsistencies of drug naming within and among regulatory agencies worldwide; a lack of clear conceptualization of what constitutes a drug; and a lack of access to physical samples. We report here the creation of a definitive, complete, and nonredundant list of all approved molecular entities as a freely available electronic resource and a physical collection of small molecules amenable to high-throughput screening.

  3. Changing values of farm animal genomic resources. from historical breeds to the Nagoya Protocol

    PubMed Central

    Tamminen, Sakari

    2015-01-01

    The paper reviews the history of Animal genetic resources (AnGRs) and claims that over the course of history they have been conceptually transformed from economic, ecologic and scientific life forms into political objects, reflecting in the way in which any valuation of AnGRs is today inherently imbued with national politics and its values enacted by legally binding global conventions. Historically, the first calls to conservation were based on the economic, ecological and scientific values of the AnGR. While the historical arguments are valid and still commonly proposed values for conservation, the AnGR have become highly politicized since the adoption of the Convention of Biological Diversity (CBD), the subsequent Interlaken Declaration, the Global Plan for Action (GPA) and the Nagoya Protocol. The scientific and political definitions of the AnGRs were creatively reshuffled within these documents and the key criteria by which they are now identified and valued today were essentially redefined. The criteria of “in situ condition” has become the necessary starting point for all valuation efforts of AnGRs, effectively transforming their previous nature as natural property and global genetic commons into objects of national concern pertaining to territorially discrete national genetic landscapes, regulated by the sovereign powers of the parties to the global conventions. PMID:26442098

  4. Changing values of farm animal genomic resources. from historical breeds to the Nagoya Protocol.

    PubMed

    Tamminen, Sakari

    2015-01-01

    The paper reviews the history of Animal genetic resources (AnGRs) and claims that over the course of history they have been conceptually transformed from economic, ecologic and scientific life forms into political objects, reflecting in the way in which any valuation of AnGRs is today inherently imbued with national politics and its values enacted by legally binding global conventions. Historically, the first calls to conservation were based on the economic, ecological and scientific values of the AnGR. While the historical arguments are valid and still commonly proposed values for conservation, the AnGR have become highly politicized since the adoption of the Convention of Biological Diversity (CBD), the subsequent Interlaken Declaration, the Global Plan for Action (GPA) and the Nagoya Protocol. The scientific and political definitions of the AnGRs were creatively reshuffled within these documents and the key criteria by which they are now identified and valued today were essentially redefined. The criteria of "in situ condition" has become the necessary starting point for all valuation efforts of AnGRs, effectively transforming their previous nature as natural property and global genetic commons into objects of national concern pertaining to territorially discrete national genetic landscapes, regulated by the sovereign powers of the parties to the global conventions. PMID:26442098

  5. Harnessing the sorghum genome sequence:development of a genome-wide microsattelite (SSR) resource for swift genetic mapping and map based cloning in sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sorghum is the second cereal crop to have a full genome completely sequenced (Nature (2009), 457:551). This achievement is widely recognized as a scientific milestone for grass genetics and genomics in general. However, the true worth of genetic information lies in translating the sequence informa...

  6. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

    PubMed Central

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

    2015-01-01

    The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species. PMID:26503227

  7. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei.

    PubMed

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

    2015-10-27

    The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species.

  8. Quantifying the consequences of conifer succession in aspen stands: decline in a biodiversity-supporting community.

    PubMed

    McCullough, S A; O'Geen, A T; Whiting, M L; Sarr, D A; Tate, K W

    2013-07-01

    Quaking aspen (Populus tremuloides Michaux) stands are important for biodiversity in conifer-dominated forest landscapes. Our goal was to quantify the consequences of conifer succession on understory diversity and litter quality, as well as associated changes in aspen stand condition. We studied aspen stands on national park land in the transition zone between the northern Sierra Nevada and southern Cascade mountain ranges. We field-measured ten metrics of aspen stand condition in 29 aspen stands. Along a gradient of increasing current conifer cover, we observed decreases in herbaceous species diversity and richness and an increase in forest floor O horizon depth. We interpreted aerial photos from 1952 and 1998 to determine whether directional changes in conifer cover had occurred in the stands over the past half century, and used regression modeling to associate succession with the observed range of aspen stand condition. From the period 1952 to 1998, we found that conifer encroachment occurred in half the sampled stands, with an average increase in conifer cover of 1% a year. Aspen were persistent in the remaining stands. Stand cover dynamics and percent total canopy cover interacted to influence species richness, diversity, aspen sprouting, and litter quality. In stands with conifer encroachment, both understory species richness and diversity declined. Although aspen sprouting increased, aspen establishment declined and the relative mass of woody to fine soil litter increased.

  9. Quantifying the consequences of conifer succession in aspen stands: decline in a biodiversity-supporting community.

    PubMed

    McCullough, S A; O'Geen, A T; Whiting, M L; Sarr, D A; Tate, K W

    2013-07-01

    Quaking aspen (Populus tremuloides Michaux) stands are important for biodiversity in conifer-dominated forest landscapes. Our goal was to quantify the consequences of conifer succession on understory diversity and litter quality, as well as associated changes in aspen stand condition. We studied aspen stands on national park land in the transition zone between the northern Sierra Nevada and southern Cascade mountain ranges. We field-measured ten metrics of aspen stand condition in 29 aspen stands. Along a gradient of increasing current conifer cover, we observed decreases in herbaceous species diversity and richness and an increase in forest floor O horizon depth. We interpreted aerial photos from 1952 and 1998 to determine whether directional changes in conifer cover had occurred in the stands over the past half century, and used regression modeling to associate succession with the observed range of aspen stand condition. From the period 1952 to 1998, we found that conifer encroachment occurred in half the sampled stands, with an average increase in conifer cover of 1% a year. Aspen were persistent in the remaining stands. Stand cover dynamics and percent total canopy cover interacted to influence species richness, diversity, aspen sprouting, and litter quality. In stands with conifer encroachment, both understory species richness and diversity declined. Although aspen sprouting increased, aspen establishment declined and the relative mass of woody to fine soil litter increased. PMID:23093369

  10. Low Elevation Riparian Environments: Warm-Climate Refugia for Conifers in the Great Basin, USA?

    NASA Astrophysics Data System (ADS)

    Millar, C.; Charlet, D. A.; Westfall, R. D.; Delany, D.

    2015-12-01

    The Great Basin, USA, contains hundreds of small to large mountain ranges. Many reach alpine elevations, which are separated from each other by low-elevation basins currently inhospitable to conifer growth. Many of these ranges support montane and subalpine conifer species that have affinities to the Sierra Nevada or Rocky Mountains, and from which these conifers migrated during cool periods of the Pleistocene. Under Holocene climates, the Great Basin geography became a terrestrial island-archipelago, wherein conifer populations are isolated among ranges, and inter-range migration is highly limited. During warm intervals of the Holocene, conifers would be expected to have migrated upslope following favorable conditions, and extirpation would be assumed to result from continued warming. Independent patterns, repeating across multiple species' distributions, however, suggest that refugia were present in these ranges during warm periods, and that low elevation environments below the current main distributions acted as climatic refugia. We hypothesize that cool, narrow, and north-aspect ravines, which during cool climates support persistent or seasonal creeks and deciduous riparian communities, become available as conifer habitat when warming climates desiccate creeks and deplete riparian species. We further speculate that cold-air drainage, reduced solar insolation, lower wind exposure, and higher water tables in these topographic positions support populations of montane and subalpine conifers even during warm climate intervals when high elevations are unfavorable for conifer persistence. On return to cool climates, low elevation refugia become sources for recolonizing higher slopes, and/or continue to persist as relictual populations. We present several lines of evidence supporting this hypothesis, and speculate that low-elevation, extramarginal riparian environments might act as climate refugia for Great Basin conifers in the future as well.

  11. Anaerobic activities of bacteria and fungi in moderately acidic conifer and deciduous leaf litter.

    PubMed

    Reith, Frank; Drake, Harold L; Küsel, Kirsten

    2002-07-01

    Abstract The litter layer of forest soils harbors high amounts of labile organic matter, and anaerobic decomposition processes can be initiated when oxygen is consumed more rapidly than it is supplied by diffusion. In this study, two adjacent moderately acidic forest sites, a spruce and a beech-oak forest, were selected to compare the anaerobic bacterial and fungal activities and populations of conifer and deciduous leaf litter. Most probable number (MPN) estimates of general heterotrophic aerobes and anaerobes from conifer litter equaled those from deciduous leaf litter. H(2), ethanol, formate, and lactate were initially produced with similar rates in both anoxic conifer and deciduous leaf litter microcosms. These products were rapidly consumed in deciduous leaf but not in conifer litter microcosms. Supplemental ethanol and H(2) were consumed only by deciduous leaf litter and yielded additional amounts of acetate in stoichiometries indicative of ethanol- or H(2)-dependent acetogenesis. The negligible turnover of primary fermentation products in conifer litter might be due to the low numbers of acetogens and secondary fermenters present in conifer litter compared to deciduous leaf litter. Fungi capable of anaerobic growth made up only 0.01-0.1% of the total anaerobic microorganisms cultured from conifer and deciduous leaf litter, respectively. Metabolic product profiles obtained from the highest anoxic, growth-positive MPN dilutions supplemented with antibacterial agents indicated that the dominant population of fungi, apparently mainly yeast-like cells, produced H(2), ethanol, acetate, and lactate both in conifer and deciduous leaf litter. Thus, despite acidic conditions, bacteria appear to dominate in the decomposition of carbon in anoxic microsites of both conifer and deciduous leaf litter.

  12. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

    PubMed Central

    Laing, Chad R.; Lingohr, Erika J.; Gannon, Victor P. J.; Nash, John H. E.; Taboada, Eduardo N.

    2016-01-01

    For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub

  13. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

    PubMed

    Yoshida, Catherine E; Kruczkiewicz, Peter; Laing, Chad R; Lingohr, Erika J; Gannon, Victor P J; Nash, John H E; Taboada, Eduardo N

    2016-01-01

    For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub

  14. Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations

    PubMed Central

    Lerner-Ellis, Jordan; Wang, Marina; White, Shana; Lebo, Matthew S

    2015-01-01

    Background The Canadian Open Genetics Repository is a collaborative effort for the collection, storage, sharing and robust analysis of variants reported by medical diagnostics laboratories across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important. Methods A survey to assess existing protocols for variant classification and reporting was delivered to clinical genetics laboratories across Canada. Based on feedback from this survey, a variant assessment tool was made available to all laboratories. Each participating laboratory was provided with an instance of GeneInsight, a software featuring versioning and approval processes for variant assessments and interpretations and allowing for variant data to be shared between instances. Guidelines were established for sharing data among clinical laboratories and in the final outreach phase, data will be made readily available to patient advocacy groups for general use. Results The survey demonstrated the need for improved standardisation and data sharing across the country. A variant assessment template was made available to the community to aid with standardisation. Instances of the GeneInsight tool were provided to clinical diagnostic laboratories across Canada for the purpose of uploading, transferring, accessing and sharing variant data. Conclusions As an ongoing endeavour and a permanent resource, the Canadian Open Genetics Repository aims to serve as a focal point for the collaboration of Canadian laboratories with other countries in the development of tools that take full advantage of laboratory data in diagnosing, managing and treating genetic diseases. PMID:25904639

  15. Cyclic voltammetric study of Co-Ni-Fe alloys electrodeposition in sulfate medium

    SciTech Connect

    Hanafi, I.; Daud, A. R.; Radiman, S.

    2013-11-27

    Electrochemical technique has been used to study the electrodeposition of cobalt, nickel, iron and Co-Ni-Fe alloy on indium tin oxide (ITO) coated glass substrate. To obtain the nucleation mechanism, cyclic voltammetry is used to characterize the Co-Ni-Fe system. The scanning rate effect on the deposition process was investigated. Deposition of single metal occurs at potential values more positive than that estimated stability potential. Based on the cyclic voltammetry results, the electrodeposition of cobalt, nickel, iron and Co-Ni-Fe alloy clearly show that the process of diffusion occurs is controlled by the typical nucleation mechanism.

  16. Controls over hydrocarbon emissions from boreal forest conifers

    SciTech Connect

    Lerdau, M.; Litvak, M.; Monson, R. |

    1995-06-01

    The emissions of monoterpenes and isoprene were measured from two species of conifers native to the boreal forest of Canada, jack pine, Pinus rigida, and black spruce, Picea Mariana. We examined the effects of phenology and needle age on the emissions of these compounds, and the variations in tissue concentrations of monoterpenes. We measured photosynthetic carbon uptake and hydrocarbon emissions at two sites in northern Saskatchewan under controlled light, temperatures, and CO{sub 2} concentrations, and analyzed carbon uptake rates using an infra-red gas analyzer and hydrocarbon emissions using a solid sorbent/thermal desorption system coupled to a gas chromatograph with a mass spectrometer. Our data indicate a strong effect of temperature and seasonality on emissions but only small effects of site conditions. These results suggest that regional models of hydrocarbon emissions from boreal forests should focus on temperature and phenology as the most important controlling variables.

  17. In-vitro Antimicrobial Activities of Some Iranian Conifers

    PubMed Central

    Afsharzadeh, Maryam; Naderinasab, Mahboobe; Tayarani Najaran, Zahra; Barzin, Mohammad; Emami, Seyed Ahmad

    2013-01-01

    Male and female leaves and fruits of eleven different taxons of Iranian conifers (Cupressus sempervirens var. horizontalis, C. sempervirens var. sempervirens, C. sempervirens cv. Cereifeormis, Juniperus communis subsp. hemisphaerica, J. excelsa subsp. excelsa, J. excelsa subsp. polycarpos, J. foetidissima, J. oblonga, J. sabina, Platycladus orientalis and Taxus baccata) were collected from different localities of Iran, dried and extracted with methanol. The extracts were tested for their antimicrobial activity against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli and Candida albicans. The extracts were screened qualitatively using four different methods, the disc diffusion, hole plate, cylinder agar diffusion and agar dilution methods, whereas the minimum inhibitory concentrations (MIC) of each extract were determined by the agar dilution method. The best result was obtained by means of hole plate method in qualitative determination of antimicrobial activities of extracts and the greatest activity was found against S. aureus in all tested methods. PMID:24250573

  18. Examining historical and current mixed-severity fire regimes in ponderosa pine and mixed-conifer forests of western North America.

    PubMed

    Odion, Dennis C; Hanson, Chad T; Arsenault, André; Baker, William L; Dellasala, Dominick A; Hutto, Richard L; Klenner, Walt; Moritz, Max A; Sherriff, Rosemary L; Veblen, Thomas T; Williams, Mark A

    2014-01-01

    There is widespread concern that fire exclusion has led to an unprecedented threat of uncharacteristically severe fires in ponderosa pine (Pinus ponderosa Dougl. ex. Laws) and mixed-conifer forests of western North America. These extensive montane forests are considered to be adapted to a low/moderate-severity fire regime that maintained stands of relatively old trees. However, there is increasing recognition from landscape-scale assessments that, prior to any significant effects of fire exclusion, fires and forest structure were more variable in these forests. Biota in these forests are also dependent on the resources made available by higher-severity fire. A better understanding of historical fire regimes in the ponderosa pine and mixed-conifer forests of western North America is therefore needed to define reference conditions and help maintain characteristic ecological diversity of these systems. We compiled landscape-scale evidence of historical fire severity patterns in the ponderosa pine and mixed-conifer forests from published literature sources and stand ages available from the Forest Inventory and Analysis program in the USA. The consensus from this evidence is that the traditional reference conditions of low-severity fire regimes are inaccurate for most forests of western North America. Instead, most forests appear to have been characterized by mixed-severity fire that included ecologically significant amounts of weather-driven, high-severity fire. Diverse forests in different stages of succession, with a high proportion in relatively young stages, occurred prior to fire exclusion. Over the past century, successional diversity created by fire decreased. Our findings suggest that ecological management goals that incorporate successional diversity created by fire may support characteristic biodiversity, whereas current attempts to "restore" forests to open, low-severity fire conditions may not align with historical reference conditions in most ponderosa

  19. Examining historical and current mixed-severity fire regimes in ponderosa pine and mixed-conifer forests of western North America.

    PubMed

    Odion, Dennis C; Hanson, Chad T; Arsenault, André; Baker, William L; Dellasala, Dominick A; Hutto, Richard L; Klenner, Walt; Moritz, Max A; Sherriff, Rosemary L; Veblen, Thomas T; Williams, Mark A

    2014-01-01

    There is widespread concern that fire exclusion has led to an unprecedented threat of uncharacteristically severe fires in ponderosa pine (Pinus ponderosa Dougl. ex. Laws) and mixed-conifer forests of western North America. These extensive montane forests are considered to be adapted to a low/moderate-severity fire regime that maintained stands of relatively old trees. However, there is increasing recognition from landscape-scale assessments that, prior to any significant effects of fire exclusion, fires and forest structure were more variable in these forests. Biota in these forests are also dependent on the resources made available by higher-severity fire. A better understanding of historical fire regimes in the ponderosa pine and mixed-conifer forests of western North America is therefore needed to define reference conditions and help maintain characteristic ecological diversity of these systems. We compiled landscape-scale evidence of historical fire severity patterns in the ponderosa pine and mixed-conifer forests from published literature sources and stand ages available from the Forest Inventory and Analysis program in the USA. The consensus from this evidence is that the traditional reference conditions of low-severity fire regimes are inaccurate for most forests of western North America. Instead, most forests appear to have been characterized by mixed-severity fire that included ecologically significant amounts of weather-driven, high-severity fire. Diverse forests in different stages of succession, with a high proportion in relatively young stages, occurred prior to fire exclusion. Over the past century, successional diversity created by fire decreased. Our findings suggest that ecological management goals that incorporate successional diversity created by fire may support characteristic biodiversity, whereas current attempts to "restore" forests to open, low-severity fire conditions may not align with historical reference conditions in most ponderosa

  20. Examining Historical and Current Mixed-Severity Fire Regimes in Ponderosa Pine and Mixed-Conifer Forests of Western North America

    PubMed Central

    Odion, Dennis C.; Hanson, Chad T.; Arsenault, André; Baker, William L.; DellaSala, Dominick A.; Hutto, Richard L.; Klenner, Walt; Moritz, Max A.; Sherriff, Rosemary L.; Veblen, Thomas T.; Williams, Mark A.

    2014-01-01

    There is widespread concern that fire exclusion has led to an unprecedented threat of uncharacteristically severe fires in ponderosa pine (Pinus ponderosa Dougl. ex. Laws) and mixed-conifer forests of western North America. These extensive montane forests are considered to be adapted to a low/moderate-severity fire regime that maintained stands of relatively old trees. However, there is increasing recognition from landscape-scale assessments that, prior to any significant effects of fire exclusion, fires and forest structure were more variable in these forests. Biota in these forests are also dependent on the resources made available by higher-severity fire. A better understanding of historical fire regimes in the ponderosa pine and mixed-conifer forests of western North America is therefore needed to define reference conditions and help maintain characteristic ecological diversity of these systems. We compiled landscape-scale evidence of historical fire severity patterns in the ponderosa pine and mixed-conifer forests from published literature sources and stand ages available from the Forest Inventory and Analysis program in the USA. The consensus from this evidence is that the traditional reference conditions of low-severity fire regimes are inaccurate for most forests of western North America. Instead, most forests appear to have been characterized by mixed-severity fire that included ecologically significant amounts of weather-driven, high-severity fire. Diverse forests in different stages of succession, with a high proportion in relatively young stages, occurred prior to fire exclusion. Over the past century, successional diversity created by fire decreased. Our findings suggest that ecological management goals that incorporate successional diversity created by fire may support characteristic biodiversity, whereas current attempts to “restore” forests to open, low-severity fire conditions may not align with historical reference conditions in most ponderosa

  1. Uniform versus asymmetric shading mediates crown recession in conifers.

    PubMed

    Schoonmaker, Amanda L; Lieffers, Victor J; Landhäusser, Simon M

    2014-01-01

    In this study we explore the impact of asymmetrical vs. uniform crown shading on the mortality and growth of upper and lower branches within tree crowns, for two conifer species: shade intolerant lodgepole pine (Pinus contorta) and shade tolerant white spruce (Picea glauca). We also explore xylem hydraulics, foliar nutrition, and carbohydrate status as drivers for growth and expansion of the lower and upper branches in various types of shading. This study was conducted over a two-year period across 10 regenerating forest sites dominated by lodgepole pine and white spruce, in the lower foothills of Alberta, Canada. Trees were assigned to one of four shading treatments: (1), complete uniform shading of the entire tree, (2) light asymmetric shading where the lower 1/4-1/3 of the tree crown was shaded, (3) heavy asymmetric shading as in (2) except with greater light reduction and (4) control in which no artificial shading occurred and most of the entire crown was exposed to full light. Asymmetrical shading of only the lower crown had a larger negative impact on the bud expansion and growth than did uniform shading, and the effect was stronger in pine relative to spruce. In addition, lower branches in pine also had lower carbon reserves, and reduced xylem-area specific conductivity compared to spruce. For both species, but particularly the pine, the needles of lower branches tended to store less C than upper branches in the asymmetric shade, which could suggest a movement of reserves away from the lower branches. The implications of these findings correspond with the inherent shade tolerance and self-pruning behavior of these conifers and supports a carbon based mechanism for branch mortality--mediated by an asymmetry in light exposure of the crown. PMID:25136823

  2. Uniform versus asymmetric shading mediates crown recession in conifers.

    PubMed

    Schoonmaker, Amanda L; Lieffers, Victor J; Landhäusser, Simon M

    2014-01-01

    In this study we explore the impact of asymmetrical vs. uniform crown shading on the mortality and growth of upper and lower branches within tree crowns, for two conifer species: shade intolerant lodgepole pine (Pinus contorta) and shade tolerant white spruce (Picea glauca). We also explore xylem hydraulics, foliar nutrition, and carbohydrate status as drivers for growth and expansion of the lower and upper branches in various types of shading. This study was conducted over a two-year period across 10 regenerating forest sites dominated by lodgepole pine and white spruce, in the lower foothills of Alberta, Canada. Trees were assigned to one of four shading treatments: (1), complete uniform shading of the entire tree, (2) light asymmetric shading where the lower 1/4-1/3 of the tree crown was shaded, (3) heavy asymmetric shading as in (2) except with greater light reduction and (4) control in which no artificial shading occurred and most of the entire crown was exposed to full light. Asymmetrical shading of only the lower crown had a larger negative impact on the bud expansion and growth than did uniform shading, and the effect was stronger in pine relative to spruce. In addition, lower branches in pine also had lower carbon reserves, and reduced xylem-area specific conductivity compared to spruce. For both species, but particularly the pine, the needles of lower branches tended to store less C than upper branches in the asymmetric shade, which could suggest a movement of reserves away from the lower branches. The implications of these findings correspond with the inherent shade tolerance and self-pruning behavior of these conifers and supports a carbon based mechanism for branch mortality--mediated by an asymmetry in light exposure of the crown.

  3. Uniform versus Asymmetric Shading Mediates Crown Recession in Conifers

    PubMed Central

    Schoonmaker, Amanda L.; Lieffers, Victor J.; Landhäusser, Simon M.

    2014-01-01

    In this study we explore the impact of asymmetrical vs. uniform crown shading on the mortality and growth of upper and lower branches within tree crowns, for two conifer species: shade intolerant lodgepole pine (Pinus contorta) and shade tolerant white spruce (Picea glauca). We also explore xylem hydraulics, foliar nutrition, and carbohydrate status as drivers for growth and expansion of the lower and upper branches in various types of shading. This study was conducted over a two-year period across 10 regenerating forest sites dominated by lodgepole pine and white spruce, in the lower foothills of Alberta, Canada. Trees were assigned to one of four shading treatments: (1), complete uniform shading of the entire tree, (2) light asymmetric shading where the lower 1/4–1/3 of the tree crown was shaded, (3) heavy asymmetric shading as in (2) except with greater light reduction and (4) control in which no artificial shading occurred and most of the entire crown was exposed to full light. Asymmetrical shading of only the lower crown had a larger negative impact on the bud expansion and growth than did uniform shading, and the effect was stronger in pine relative to spruce. In addition, lower branches in pine also had lower carbon reserves, and reduced xylem-area specific conductivity compared to spruce. For both species, but particularly the pine, the needles of lower branches tended to store less C than upper branches in the asymmetric shade, which could suggest a movement of reserves away from the lower branches. The implications of these findings correspond with the inherent shade tolerance and self-pruning behavior of these conifers and supports a carbon based mechanism for branch mortality – mediated by an asymmetry in light exposure of the crown. PMID:25136823

  4. Morphological and functional stasis in mycorrhizal root nodules as exhibited by a Triassic conifer.

    PubMed

    Schwendemann, Andrew B; Decombeix, Anne-Laure; Taylor, Thomas N; Taylor, Edith L; Krings, Michael

    2011-08-16

    Mycorrhizal root nodules occur in the conifer families Araucariaceae, Podocarpaceae, and Sciadopityaceae. Although the fossil record of these families can be traced back into the early Mesozoic, the oldest fossil evidence of root nodules previously came from the Cretaceous. Here we report on cellularly preserved root nodules of the early conifer Notophytum from Middle Triassic permineralized peat of Antarctica. These fossil root nodules contain fungal arbuscules, hyphal coils, and vesicles in their cortex. Numerous glomoid-type spores are found in the peat matrix surrounding the nodules. This discovery indicates that mutualistic associations between conifer root nodules and arbuscular mycorrhizal fungi date back to at least the early Mesozoic, the period during which most of the modern conifer families first appeared. Notophytum root nodules predate the next known appearance of this association by 100 million years, indicating that this specialized form of mycorrhizal symbiosis has ancient origins.

  5. Morphological and functional stasis in mycorrhizal root nodules as exhibited by a Triassic conifer

    PubMed Central

    Schwendemann, Andrew B.; Decombeix, Anne-Laure; Taylor, Thomas N.; Krings, Michael

    2011-01-01

    Mycorrhizal root nodules occur in the conifer families Araucariaceae, Podocarpaceae, and Sciadopityaceae. Although the fossil record of these families can be traced back into the early Mesozoic, the oldest fossil evidence of root nodules previously came from the Cretaceous. Here we report on cellularly preserved root nodules of the early conifer Notophytum from Middle Triassic permineralized peat of Antarctica. These fossil root nodules contain fungal arbuscules, hyphal coils, and vesicles in their cortex. Numerous glomoid-type spores are found in the peat matrix surrounding the nodules. This discovery indicates that mutualistic associations between conifer root nodules and arbuscular mycorrhizal fungi date back to at least the early Mesozoic, the period during which most of the modern conifer families first appeared. Notophytum root nodules predate the next known appearance of this association by 100 million years, indicating that this specialized form of mycorrhizal symbiosis has ancient origins. PMID:21808011

  6. Biomass in conifer plantations of northeastern Minnesota. Forest Service research paper

    SciTech Connect

    Ohmann, L.F.

    1985-10-01

    The report provides biomass estimates for vegetative strata and herb-low shrub species for 53 conifer plantations in NE Minnesota. The estimates are analyzed by plantation age and silvicultural practices used to establish and release the plantations.

  7. Morphological and functional stasis in mycorrhizal root nodules as exhibited by a Triassic conifer.

    PubMed

    Schwendemann, Andrew B; Decombeix, Anne-Laure; Taylor, Thomas N; Taylor, Edith L; Krings, Michael

    2011-08-16

    Mycorrhizal root nodules occur in the conifer families Araucariaceae, Podocarpaceae, and Sciadopityaceae. Although the fossil record of these families can be traced back into the early Mesozoic, the oldest fossil evidence of root nodules previously came from the Cretaceous. Here we report on cellularly preserved root nodules of the early conifer Notophytum from Middle Triassic permineralized peat of Antarctica. These fossil root nodules contain fungal arbuscules, hyphal coils, and vesicles in their cortex. Numerous glomoid-type spores are found in the peat matrix surrounding the nodules. This discovery indicates that mutualistic associations between conifer root nodules and arbuscular mycorrhizal fungi date back to at least the early Mesozoic, the period during which most of the modern conifer families first appeared. Notophytum root nodules predate the next known appearance of this association by 100 million years, indicating that this specialized form of mycorrhizal symbiosis has ancient origins. PMID:21808011

  8. Construction of a genome-wide human BAC-Unigene resource. Final progress report, 1989--1996

    SciTech Connect

    Lim, C.S.; Xu, R.X.; Wang, M.

    1996-12-31

    Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes (non-redundant, unigene sets of cDNA representing EST clusters) are available for human alone. A total of 44,000 Unigene cDNA clones have been supplied by Research Genetics. Unigenes, or cDNAs are excellent resource for map building for two reasons. Firstly, they exist in two alternative forms -- as both sequence information for PCR primer pairs, and cDNA clones -- thus making library screening by colony hybridization as well as pooled library PCR possible. The authors have developed an efficient and robust procedure to screen genomic libraries with large number of DNA probes. Secondly, the linkage and order of expressed sequences, or genes are highly conserved among human, mouse and other mammalian species. Therefore, mapping with cDNA markers rather than random anonymous STSs will greatly facilitate comparative, evolutionary studies as well as physical map building. They have currently deconvoluted over 10,000 Unigene probes against a 4X coverage human BAC clones from the approved library D by high density colony hybridization method. 10,000 batches of Unigenes are arrayed in an imaginary 100 X 100 matrix from which 100 row pools and 100 column pools are obtained. Library filters are hybridized with pooled probes, thus reducing the number of hybridization required for addressing the positives for each Unigene from 10,000 to 200. Details on the experimental scheme as well as daily progress report is posted on the Web site (http://www.tree.caltech.edu).

  9. Ungulate exclusion, conifer thinning and mule deer forage in northeastern New Mexico

    USGS Publications Warehouse

    Kramer, David W.; Sorensen, Grant E.; Taylor, Chase A.; Cox, Robert D.; Gipson, Philip S.; Cain, James W.

    2015-01-01

    The southwestern United States has experienced expansion of conifer species (Juniperus spp. and Pinus ponderosa) into areas of semi-arid grassland over the past century. The expansion of conifers can limit palatable forage and reduce grass and forb communities. Conifer species are sometimes thinned through hydraulic mulching or selective cutting. We assessed the effects of these treatments on mule deer (Odocoileus hemionus) habitat in northeastern New Mexico to determine if conifer thinning improved cover of preferred forage species for mule deer in areas with and without ungulates. We measured plant cover and occurrence of preferred forage species in the summers of 2011 and 2012. An ongoing regional drought probably reduced vegetation response, with preferred forage species and herbaceous cover responding to conifer thinning or ungulate exclusion immediately following treatment, but not the following year. In 2011, areas that received thinning treatments had a higher abundance of preferred forage when compared to sites with no treatment. Grass coverage exhibited an immediate response in 2011, with ungulate exclosures containing 8% more coverage than areas without exclosures. The results suggest that conifer thinning and ungulate exclusion may elicit a positive response, however in the presence of drought; the positive effects are only short-term.

  10. Evolutionary assembly of the conifer fauna: distinguishing ancient from recent associations in bark beetles.

    PubMed Central

    Sequeira, A S; Normark, B B; Farrell, B D

    2000-01-01

    Several shifts from ancestral conifer feeding to angiosperm feeding have been implicated in the unparalleled diversification of beetle species. The single largest angiosperm-feeding beetle clade occurs in the weevils, and comprises the family Curculionidae and relatives. Most authorities confidently place the bark beetles (Scolytidae) within this radiation of angiosperm feeders. However, some clues indicate that the association between conifers and some scolytids, particularly in the tribe Tomicini, is a very ancient one. For instance, several fragments of Gondwanaland (South America, New Caledonia, Australia and New Guinea) harbour endemic Tomicini specialized on members of the formerly widespread and abundant conifer family Araucariaceae. As a first step towards resolving this seeming paradox, we present a phylogenetic analysis of the beetle family Scolytidae with particularly intensive sampling of conifer-feeding Tomicini and allies. We sequenced and analysed elongation factor 1alpha and nuclear rDNAs 18S and 28S for 45 taxa, using members of the weevil family Cossoninae as an out-group. Our results indicate that conifer feeding is the ancestral host association of scolytids, and that the most basal lineages of scolytids feed on Aramucaria. If scolytids are indeed nested within a great angiosperm-feeding clade, as many authorities have held, then a reversion to conifer feeding in ancestral scolytids appears to have occurred in the Mesozoic, when Araucaria still formed a major component of the woody flora. PMID:11133024

  11. Applying genomic and bioinformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery.

    PubMed

    Seto, Jason; Walsh, Michael P; Mahadevan, Padmanabhan; Zhang, Qiwei; Seto, Donald

    2010-01-01

    Technological advances and increasingly cost-effect methodologies in DNA sequencing and computational analysis are providing genome and proteome data for human adenovirus research. Applying these tools, data and derived knowledge to the development of vaccines against these pathogens will provide effective prophylactics. The same data and approaches can be applied to vector development for gene delivery in gene therapy and vaccine delivery protocols. Examination of several field strain genomes and their analyses provide examples of data that are available using these approaches. An example of the development of HAdV-B3 both as a vaccine and also as a vector is presented.

  12. Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides1

    PubMed Central

    Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

    2015-01-01

    Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species. PMID:26421250

  13. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic mode...

  14. Fluxes of trichloroacetic acid through a conifer forest canopy.

    PubMed

    Stidson, R T; Heal, K V; Dickey, C A; Cape, J N; Heal, M R

    2004-11-01

    Controlled-dosing experiments with conifer seedlings have demonstrated an above-ground route of uptake for trichloroacetic acid (TCA) from aqueous solution into the canopy, in addition to uptake from the soil. The aim of this work was to investigate the loss of TCA to the canopy in a mature conifer forest exposed only to environmental concentrations of TCA by analysing above- and below-canopy fluxes of TCA and within-canopy instantaneous reservoir of TCA. Concentrations and fluxes of TCA were quantified for one year in dry deposition, rainwater, cloudwater, throughfall, stemflow and litterfall in a 37-year-old Sitka spruce and larch plantation in SW Scotland. Above-canopy TCA deposition was dominated by rainfall (86%), compared with cloudwater (13%) and dry deposition (1%). On average only 66% of the TCA deposition passed through the canopy in throughfall and stemflow (95% and 5%, respectively), compared with 47% of the wet precipitation depth. Consequently, throughfall concentration of TCA was, on average, approximately 1.4 x rainwater concentration. There was no significant difference in below-canopy fluxes between Sitka spruce and larch, or at a forest-edge site. Annual TCA deposited from the canopy in litterfall was only approximately 1-2% of above-canopy deposition. On average, approximately 800 microg m(-2) of deposited TCA was lost to the canopy per year, compared with estimates of above-ground TCA storage of approximately 400 and approximately 300 microg m(-2) for Sitka spruce and larch, respectively. Taking into account likely uncertainties in these values ( approximately +/- 50%), these data yield an estimate for the half-life of within-canopy elimination of TCA in the range 50-200 days, assuming steady-state conditions and that all TCA lost to the canopy is transferred into the canopy material, rather than degraded externally. The observations provide strong indication that an above-ground route is important for uptake of TCA specifically of atmospheric

  15. Assessed Potential of Conifers as Proxy Paleo-wind Stations

    NASA Astrophysics Data System (ADS)

    Hamilton, W. L.

    2002-12-01

    A new method for extracting wind direction and velocity information from tree rings has been developed and applied to more than 60 conifers near two weather stations on the Olympic Peninsula of northwest Washington. Utilizing measurements from cores and full cross-sections, a mechanical wind-drag bending-moment model relates ring eccentricity to the horizontal component of unbalanced forces, principally wind, affecting the tree. Straight conifers on level ground typically develop thicker rings on the downwind side. The two study areas have very different wind patterns. At Port Angeles dominant wind is the westerly sea breeze, but at Quillayute dominant winds are southeast and southwest. Tested weather station record wind parameters include: annual (and seasonal) mean and summed velocity for hourly or peak daily observations. Sum velocity yields much higher significance than mean velocity in regressions against growth eccentricity, suggesting that tree response may be related to momentum transfer. Correlation significance increases when a 3-year running mean is applied to smooth out measurement error, delayed response to wind, and spatial wind variability; and when several trees are averaged, dispersing events such as limb loss. Linear regression of the vector resultants of eccentricity of Douglas-fir against annual sum velocity vector records at Port Angeles yields significant (P(t)<0.05) slope constants for R and θ in most cases. Vector assessment of Sitka spruce near Quillayute is limited by multimodal wind. Scalar sum velocity and ring-width eccentricity data from these and other species are significantly correlated at both areas. Seasonal assessment of eccentricity response to wind at the Pacific coast suggests that very high velocities, especially during growth season, promote thinner rings on the downwind side. In such cases predicted response is delayed by up to 8 years. Rainfall is a significant co-contributor to eccentricity only at the wetter coastal

  16. Measured and Predicted Solar Transmission Through Conifer Canopies

    NASA Astrophysics Data System (ADS)

    Hardy, J. P.; Marks, D.; Melloh, R.; Winstral, A.; Koenig, G.

    2003-12-01

    Snow dynamics under forest canopies are strongly influenced by the large spatial variability of energy transfers in this environment. Transmission of solar radiation through a canopy is highly variable and depends on tree species, as well as canopy properties such as height, density, and leaf area. Modeling snow processes at the stand scale has proven challenging due to the highly variable structure of forest canopies controlling solar radiation incident at the snow surface. This study aims to describe and simulate the solar irradiance variability on the snow surface beneath two stands: an open, discontinuous conifer canopy, and a relatively uniform conifer canopy. The objectives are 1) to compare measured and predicted solar transmissivities based on field data and analysis of hemispherical photographs and 2) to evaluate the magnitude of the predicted solar fluxes and the timing of snow ablation using the snow model, SNOBAL, driven separately with both measured and modeled solar transmissivities. Field measurements were made during winters of 2002 and 2003 at the Local Scale Observation Site (LSOS) in Fraser, Colorado USA as part of the Cold Land Processes Experiment. The canopy structure of the trees in a 0.8 ha plot was measured in detail (species, tree location, height, crown height, diameter at breast height). We measured incoming global solar radiation at the snow surface, beneath uniform and discontinuous lodgepole pine canopies, using arrays of 10 upward looking pyranometers at each site. Incoming global solar radiation was measured above the canopy and used to calculate transmitted values. Hemispherical photographs taken, with a Nikon CoolPix995 digital camera equipped with a Nikon Fisheye Converter (183° FOV), at each pyranometer location (n=20) were analyzed with Gap Light Analyzer (GLA) software (Frazer, et al. 1999) to determine total solar transmissivity. Mean measured and predicted solar transmissivities compared well (r2=0.86) in the discontinuous

  17. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

    PubMed

    Seaver, Samuel M D; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M T; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D; Henry, Christopher S

    2014-07-01

    The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed. PMID:24927599

  18. Conifer flavonoid compounds inhibit detoxification enzymes and synergize insecticides.

    PubMed

    Wang, Zhiling; Zhao, Zhong; Cheng, Xiaofei; Liu, Suqi; Wei, Qin; Scott, Ian M

    2016-02-01

    Detoxification by glutathione S-transferases (GSTs) and esterases are important mechanisms associated with insecticide resistance. Discovery of novel GST and esterase inhibitors from phytochemicals could provide potential new insecticide synergists. Conifer tree species contain flavonoids, such as taxifolin, that inhibit in vitro GST activity. The objectives were to test the relative effectiveness of taxifolin as an enzyme inhibitor and as an insecticide synergist in combination with the organophosphorous insecticide, Guthion (50% azinphos-methyl), and the botanical insecticide, pyrethrum, using an insecticide-resistant Colorado potato beetle (CPB) Leptinotarsa decemlineata (Say) strain. Both taxifolin and its isomer, quercetin, increased the mortality of 1(st) instar CPB larvae after 48h when combined with Guthion, but not pyrethrum. Taxifolin had greater in vitro esterase inhibition compared with the commonly used esterase inhibitor, S, S, S-tributyl phosphorotrithioate (DEF). An in vivo esterase and GST inhibition effect after ingestion of taxifolin was measured, however DEF caused a greater suppression of esterase activity. This study demonstrated that flavonoid compounds have both in vitro and in vivo esterase inhibition, which is likely responsible for the insecticide synergism observed in insecticide-resistant CPB. PMID:26821651

  19. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers.

    PubMed

    Pascual, María B; El-Azaz, Jorge; de la Torre, Fernando N; Cañas, Rafael A; Avila, Concepción; Cánovas, Francisco M

    2016-01-01

    The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined. PMID:27468292

  20. Advances in Conifer Somatic Embryogenesis Since Year 2000.

    PubMed

    Klimaszewska, Krystyna; Hargreaves, Catherine; Lelu-Walter, Marie-Anne; Trontin, Jean-François

    2016-01-01

    This review compiles research results published over the last 14 years on conifer somatic embryogenesis (SE). Emphasis is placed on the newest findings that affect the response of seed embryos (typical explants) and shoot primordia (rare explants) to the induction of SE and long-term culture of early somatic embryos. Much research in recent years has focused on maturation of somatic embryos, with respect to both yield and quality, as an important stage for the production of a large number of vigorous somatic seedlings. Attempts to scale up somatic embryo production numbers and handling have resulted in a few bioreactor designs, the utility of which may prove beneficial for an industrial application. A few simplified cryopreservation methods for embryonal masses (EM) were developed as a means to ensure cost-efficient long-term storage of genotypes during clonal field testing. Finally, recent long-term studies on the growth of somatic trees in the field, including seed production yield and comparison of seed parameters produced by somatic versus seed-derived trees, are described.

  1. Conservative water management in the widespread conifer genus Callitris

    PubMed Central

    Brodribb, Timothy J.; Bowman, David M. J. S.; Grierson, Pauline F.; Murphy, Brett P.; Nichols, Scott; Prior, Lynda D.

    2013-01-01

    Water management by woody species encompasses characters involved in seeking, transporting and evaporating water. Examples of adaptation of individual characters to water availability are common, but little is known about the adaptability of whole-plant water management. Here we use plant hydration and growth to examine variation in whole-plant water management characteristics within the conifer genus Callitris. Using four species that cover the environmental extremes in the Australian continent, we compare seasonal patterns of growth and hydration over 2 years to determine the extent to which species exhibit adaptive variation to the local environment. Detailed measurements of gas exchange in one species are used to produce a hydraulic model to predict changes in leaf water potential throughout the year. This same model, when applied to the remaining three species, provided a close representation of the measured patterns of water potential gradient at all sites, suggesting strong conservation in water management, a conclusion supported by carbon and oxygen isotope measurements in Callitris from across the continent. We conclude that despite its large range in terms of rainfall, Callitris has a conservative water management strategy, characterized by a high sensitivity of growth to rainfall and a delayed (anisohydric) closure of stomata during soil drying.

  2. Effects of acid fog and ozone on conifers. Final report

    SciTech Connect

    Bytnerowicz, A.; Olszyk, D.M.; Takemoto, B.K.; McCool, P.M.; Musselman, R.C.

    1989-05-01

    This study evaluated the effects of acidic fog (pH 2.0, 3.0, or 4.0) on the physiological, biochemical, and growth responses of two coniferous tree species (Pinus ponderosa and Abies concolor), and determined if exposure to acidic fog predisposed the tree seedlings to the phytotoxic effects of ozone (O{sub 3}). Results provide evidence that the growth and metabolic responses of two coniferous tree species could be altered by multiple applications of acidic fog, and by exposure to ambient O{sub 3}. In general, the alterations were slight to modest, which may be attributed to the low degree of stress severity, and the slow rate of tree growth. The findings indicate that exposure to acidic fog followed by O{sub 3} does not cause detectable changes in conifer seedling growth within a single-growing season. Nevertheless, it is clear that acidic fog and O{sub 3} cause temporal alterations in seedling physiology and biochemistry.

  3. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers

    PubMed Central

    Pascual, María B.; El-Azaz, Jorge; de la Torre, Fernando N.; Cañas, Rafael A.; Avila, Concepción; Cánovas, Francisco M.

    2016-01-01

    The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined. PMID:27468292

  4. Complete tylosis formation in a latest Permian conifer stem

    PubMed Central

    Feng, Zhuo; Wang, Jun; Rößler, Ronny; Kerp, Hans; Wei, Hai-Bo

    2013-01-01

    Background and Aims Our knowledge of tylosis formation is mainly based on observations of extant plants; however, its developmental and functional significance are less well understood in fossil plants. This study, for the first time, describes a complete tylosis formation in a fossil woody conifer and discusses its ecophysiological implications. Methods The permineralized stem of Shenoxylon mirabile was collected from the upper Permian (Changhsingian) Sunjiagou Formation of Shitanjing coalfield, northern China. Samples from different portions of the stem were prepared by using the standard thin-sectioning technique and studied in transmitted light. Key Results The outgrowth of ray parenchyma cells protruded into adjacent tracheids through pits initially forming small pyriform or balloon-shaped structures, which became globular or slightly elongated when they reached their maximum size. The tracheid luminae were gradually occluded by densely spaced tyloses. The host tracheids are arranged in distinct concentric zones representing different growth phases of tylosis formation within a single growth ring. Conclusions The extensive development of tyloses from the innermost heartwood (metaxylem) tracheids to the outermost sapwood tracheids suggests that the plant was highly vulnerable and reacted strongly to environmental stress. Based on the evidence available, the tyloses were probably not produced in response to wound reaction or pathogenic infection, since evidence of wood traumatic events or fungal invasion are not recognizable. Rather, they may represent an ecophysiological response to the constant environmental stimuli. PMID:23532049

  5. Modeling acclimation of photosynthesis to temperature in evergreen conifer forests.

    PubMed

    Gea-Izquierdo, Guillermo; Mäkelä, Annikki; Margolis, Hank; Bergeron, Yves; Black, T Andrew; Dunn, Allison; Hadley, Julian; Kyaw Tha Paw U; Falk, Matthias; Wharton, Sonia; Monson, Russell; Hollinger, David Y; Laurila, Tuomas; Aurela, Mika; McCaughey, Harry; Bourque, Charles; Vesala, Timo; Berninger, Frank

    2010-10-01

    • In this study, we used a canopy photosynthesis model which describes changes in photosynthetic capacity with slow temperature-dependent acclimations. • A flux-partitioning algorithm was applied to fit the photosynthesis model to net ecosystem exchange data for 12 evergreen coniferous forests from northern temperate and boreal regions. • The model accounted for much of the variation in photosynthetic production, with modeling efficiencies (mean > 67%) similar to those of more complex models. The parameter describing the rate of acclimation was larger at the northern sites, leading to a slower acclimation of photosynthesis to temperature. The response of the rates of photosynthesis to air temperature in spring was delayed up to several days at the coldest sites. Overall photosynthesis acclimation processes were slower at colder, northern locations than at warmer, more southern, and more maritime sites. • Consequently, slow changes in photosynthetic capacity were essential to explaining variations of photosynthesis for colder boreal forests (i.e. where acclimation of photosynthesis to temperature was slower), whereas the importance of these processes was minor in warmer conifer evergreen forests.

  6. Vigor loss in conifers due to dwarf mistletoe

    NASA Technical Reports Server (NTRS)

    Meyer, M. P.; French, D. W.; Latham, R. P.; Nelson, C. A.

    1970-01-01

    Practical remote sensing techniques were developed for detecting and evaluating vigor loss in forest conifers due to dwarf mistletoe. Eastern dwarf mistletoe (Arceuthobium pusillum) infection of black spruce (Picea mariana) was investigated. A tower-tramway system, 100 feet high, was erected over an infected stand in northeast Minnesota in June and multiband/multidate photography was initiated in July and is continuing. Four 70mm film-filter combinations were used in a multicamera unit: Plus-X/Wratten 58, Plus-X/Wratten 25A, Aero Infrared/Wratten 89B, and Ektachrome Infrared/Wratten 12. The stand of mistletoe-infected black spruce under the tramway was photographed three times per day (0900, 1200 and 1500 local sun time) at approximately 10 day intervals. An extensive test site, several square miles in area, was selected in north-central Minnesota for the purpose of testing photographic specifications developed on the tramway test site. One aerial photographic flight at a variety of altitudes was accomplished over the extensive test site in August. Data analyses are not available at this time.

  7. Detection of aspen/conifer forest mixes from multitemporal LANDSAT digital data. [Bear River Range, Rocky Mountains

    NASA Technical Reports Server (NTRS)

    Merola, J. A.; Jaynes, R. A.; Harniss, R. O.

    1983-01-01

    Aspen, conifer and mixed aspen/conifer forests were mapped for a 15-quadrangle study area in the Utah-Idaho Bear River Range using LANDSAT multispectral scanner (MSS) data. The digital MSS data were utilized to devise quantitative indices which correlate with apparently stable and seral aspen forests. The extent to which a two-date LANDSAT MSS analysis may permit the delineation of different categories of aspen/conifer forest mix was explored. Multitemporal analyses of MSS data led to the identification of early, early to mid, mid to late, and late seral stages of aspen/conifer forest mixing.

  8. MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

    PubMed Central

    D'Onorio de Meo, Paolo; D'Antonio, Mattia; Griggio, Francesca; Lupi, Renato; Borsani, Massimiliano; Pavesi, Giulio; Castrignanò, Tiziana; Pesole, Graziano; Gissi, Carmela

    2012-01-01

    The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. PMID:22123747

  9. MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa.

    PubMed

    D'Onorio de Meo, Paolo; D'Antonio, Mattia; Griggio, Francesca; Lupi, Renato; Borsani, Massimiliano; Pavesi, Giulio; Castrignanò, Tiziana; Pesole, Graziano; Gissi, Carmela

    2012-01-01

    The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa.

  10. New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.

    PubMed

    Faivre-Rampant, P; Zaina, G; Jorge, V; Giacomello, S; Segura, V; Scalabrin, S; Guérin, V; De Paoli, E; Aluome, C; Viger, M; Cattonaro, F; Payne, A; PaulStephenRaj, P; Le Paslier, M C; Berard, A; Allwright, M R; Villar, M; Taylor, G; Bastien, C; Morgante, M

    2016-07-01

    Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra. PMID:26929265

  11. Ensembl Genomes 2016: more genomes, more complexity

    PubMed Central

    Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  12. From amplification to gene in thyroid cancer: A high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization

    SciTech Connect

    Chen, X.N.; Gonsky, R.; Korenberg, J.R.; Knauf, J.A.; Fagin, J.A.; Chissoe, S.

    1998-08-01

    Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. The authors now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. They used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3--6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKC{epsilon}), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKC{epsilon} as a previously unmapped candidate gene involved in thyroid tumorigenesis.

  13. Structure-function constraints of tracheid-based xylem: a comparison of conifers and ferns.

    PubMed

    Pittermann, Jarmila; Limm, Emily; Rico, Christopher; Christman, Mairgareth A

    2011-10-01

    The ferns comprise one of the most ancient tracheophytic plant lineages, and occupy habitats ranging from tundra to deserts and the equatorial tropics. Like their nearest relatives the conifers, modern ferns possess tracheid-based xylem but the structure-function relationships of fern xylem are poorly understood. Here, we sampled the fronds (megaphylls) of 16 species across the fern phylogeny, and examined the relationships among hydraulic transport, drought-induced cavitation resistance, the xylem anatomy of the stipe, and the gas-exchange response of the pinnae. For comparison, the results are presented alongside a similar suite of conifer data. Fern xylem is as resistant to cavitation as conifer xylem, but exhibits none of the hydraulic or structural trade-offs associated with resistance to cavitation. On a conduit diameter basis, fern xylem can exhibit greater hydraulic efficiency than conifer and angiosperm xylem. In ferns, wide and long tracheids compensate in part for the lack of secondary xylem and allow ferns to exhibit transport rates on a par with those of conifers. We suspect that it is the arrangement of the primary xylem, in addition to the intrinsic traits of the conduits themselves, that may help explain the broad range of cavitation resistance in ferns.

  14. Mediterranean climate effects. I. Conifer water use across a Sierra Nevada ecotone.

    PubMed

    Royce, E B; Barbour, M G

    2001-05-01

    Xylem water potential of the midelevation conifers Pinus jeffreyi, Pinus lambertiana, Abies concolor, and Calocedrus decurrens, the higher elevation Pinus monticola and Abies magnifica, and co-occurring evergreen angiosperm shrubs, together with soil moisture under these plants, were monitored at three sites on the Kern Plateau in the southernmost Sierra Nevada Range of California. Site locations spanned the ecotone between the mid- and upper montane forests at elevations of 2230-2820 m. Measurements were made through a low-snowfall year and a heavy-snowfall year.In the Mediterranean climate of the Sierra Nevada, the heavy winter snowpack persists into late spring, after precipitation has effectively stopped. We found the subsequent depletion of soil moisture due to plant water uptake to result in predawn xylem water potentials for conifers more negative by 0.6-1.4 MPa than those for shrubs or inferred soil potentials. Shrubs generally depleted soil moisture more rapidly and ultimately extracted a greater fraction of the available soil moisture than did the conifers. This depletion of soil moisture by shrubs, particularly Arctostaphylos patula, may limit conifer growth and regeneration by prematurely terminating growth on the shallow soils studied. The conifers all generally showed similar patterns of soil moisture use, except that A. magnifica extracted moisture more rapidly early in the season.

  15. A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development.

    PubMed

    Mahfooz, Sahil; Singh, Satyendra P; Rakh, Ramraje; Bhattacharya, Arpita; Mishra, Nishtha; Singh, Poonam C; Chauhan, Puneet S; Nautiyal, Chandra S; Mishra, Aradhana

    2016-01-01

    Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma. PMID:27199911

  16. A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development

    PubMed Central

    Mahfooz, Sahil; Singh, Satyendra P.; Rakh, Ramraje; Bhattacharya, Arpita; Mishra, Nishtha; Singh, Poonam C.; Chauhan, Puneet S.; Nautiyal, Chandra S.; Mishra, Aradhana

    2016-01-01

    Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma. PMID:27199911

  17. A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development.

    PubMed

    Mahfooz, Sahil; Singh, Satyendra P; Rakh, Ramraje; Bhattacharya, Arpita; Mishra, Nishtha; Singh, Poonam C; Chauhan, Puneet S; Nautiyal, Chandra S; Mishra, Aradhana

    2016-01-01

    Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma.

  18. Estimating terpene and terpenoid emissions from conifer oleoresin composition

    NASA Astrophysics Data System (ADS)

    Flores, Rosa M.; Doskey, Paul V.

    2015-07-01

    The following algorithm, which is based on the thermodynamics of nonelectrolyte partitioning, was developed to predict emission rates of terpenes and terpenoids from specific storage sites in conifers: Ei =xoriγoripi∘ where Ei is the emission rate (μg C gdw-1 h-1) and pi∘ is the vapor pressure (mm Hg) of the pure liquid terpene or terpenoid, respectively, and xori and γori are the mole fraction and activity coefficient (on a Raoult's law convention), respectively, of the terpene and terpenoid in the oleoresin. Activity coefficients are calculated with Hansen solubility parameters that account for dispersive, polar, and H-bonding interactions of the solutes with the oleoresin matrix. Estimates of pi∘ at 25 °C and molar enthalpies of vaporization are made with the SIMPOL.1 method and are used to estimate pi∘ at environmentally relevant temperatures. Estimated mixing ratios of terpenes and terpenols were comparatively higher above resin-acid- and monoterpene-rich oleoresins, respectively. The results indicated a greater affinity of terpenes and terpenols for the non-functionalized and carboxylic acid containing matrix through dispersive and H-bonding interactions, which are expressed in the emission algorithm by the activity coefficient. The correlation between measured emission rates of terpenes and terpenoids for Pinus strobus and emission rates predicted with the algorithm were very good (R = 0.95). Standard errors for the range and average of monoterpene emission rates were ±6 - ±86% and ±54%, respectively, and were similar in magnitude to reported standard deviations of monoterpene composition of foliar oils (±38 - ±51% and ±67%, respectively).

  19. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum

    PubMed Central

    Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L.; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F.; Li, Shuaicheng; Hu, Kailin

    2016-01-01

    The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum. PMID:26739748

  20. Enhancing Genome-Wide Copy Number Variation Identification by High Density Array CGH Using Diverse Resources of Pig Breeds

    PubMed Central

    Wang, Jiying; Jiang, Jicai; Wang, Haifei; Kang, Huimin; Zhang, Qin; Liu, Jian-Feng

    2014-01-01

    Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs. PMID:24475311

  1. New resources for marine genomics: bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas).

    PubMed

    Cunningham, Charles; Hikima, Jun-ichi; Jenny, Matthew J; Chapman, Robert W; Fang, Guang-Chen; Saski, Chris; Lundqvist, Mats L; Wing, Rod A; Cupit, Pauline M; Gross, Paul S; Warr, Greg W; Tomkins, Jeff P

    2006-01-01

    Large-insert genomic bacterial artificial chromosome (BAC) libraries of two culturally and economically important oyster species, Crassostrea virginica and C. gigas, have been developed as part of an international effort to develop tools and reagents that will advance our ability to conduct genetic and genomic research. A total of 73,728 C. gigas clones with an average insert size of 152 kb were picked and arrayed representing an 11.8-fold genome coverage. A total of 55,296 clones with an average insert size of 150 kb were picked and arrayed for C. virginica, also representing an 11.8-fold genome coverage. The C. gigas and C. virginica libraries were screened with probes derived from selected oyster genes using high-density BAC colony filter arrays. The probes identified 4 to 25 clones per gene for C. virginica and 5 to 50 clones per gene for C. gigas. We conducted a preliminary analysis of genetic polymorphism represented in the C. gigas library. The results suggest that the degree of divergence among similar sequences is highly variable and concentrated in intronic regions. Evidence supporting allelic polymorphism is reported for two genes and allelic and/or locus specific polymorphism for several others. Classical inheritance studies are needed to confirm the nature of these polymorphisms. The oyster BAC libraries are publicly available to the research community on a cost-recovery basis at (www.genome.clemson.edu). PMID:16896533

  2. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

    PubMed

    Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

    2016-01-07

    The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

  3. The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates.

    PubMed

    Ullate-Agote, Asier; Milinkovitch, Michel C; Tzika, Athanasia C

    2014-01-01

    Squamates (snakes and lizards) exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this wide diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding of the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as a particularly appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-base paired-end reads from multiple individuals of a single family (parents and offspring) that produced a genome assembly of 1.53 gigabases (Gb), roughly covering 75% of the expected total genome size, and 297,768 scaffolds >1 Kb. We were able to fully retrieve 86, and partially another 106, of the 248 CEGMA core genes, indicating that a high genome completeness was achieved, even though the assembly is fragmented. Using MAKER2, we annotated 10,917 genes with high confidence (Annotation Edit Distance (AED)<1) and an additional 5,263 predicted genes matched with the species' transcriptome. Numerous colour and colour pattern morphs exist in P. guttatus, making it an ideal model to study the genetic determinism, development, and evolution of adaptive colour traits in reptiles. Using our draft genome and a Single-Nucleotide Polymorphism (SNP) calling approach, we confirmed the interval with the causative mutation for the amelanistic phenotype, a result supported by a parallel exome-based study.

  4. Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection

    PubMed Central

    2012-01-01

    related genes which have a homozygous genotype in the reference cohorts. This database allows the users to see which selected variants are common variants (> 5% minor allele frequency) in the Huvariome core samples, thus aiding in the selection of potentially pathogenic variants by filtering out common variants that are not listed in one of the other public genomic variation databases. The no-call rate and the accuracy of allele calling in Huvariome provides the user with the possibility of identifying platform dependent errors associated with specific regions of the human genome. Conclusion Huvariome is a simple to use resource for validation of resequencing results obtained by NGS experiments. The high sequence coverage and low error rates provide scientists with the ability to remove false positive results from pedigree studies. Results are returned via a web interface that displays location-based genetic variation frequency, impact on protein function, association with known genetic variations and a quality score of the variation base derived from Huvariome Core and the Diversity Panel data. These results may be used to identify and prioritize rare variants that, for example, might be disease relevant. In testing the accuracy of the Huvariome database, alleles of a selection of ambiguously called coding single nucleotide variants were successfully predicted in all cases. Data protection of individuals is ensured by restricted access to patient derived genomes from the host institution which is relevant for future molecular diagnostics. PMID:23164068

  5. Simulation of growth of Adirondack conifers in relation to global climate change

    SciTech Connect

    Pan, Y.; Raynal, D.J. )

    1993-06-01

    Several conifer species grown in plantations in the southeastern Adirondack mountains of New York were chosen to model tree growth. In the models, annual xylem growth was decomposed into several components that reflect various intrinsic or extrinsic factors. Growth signals indicative of climatic effects were used to construct response functions using both multivariate analysis and Kalman filter methods. Two models were used to simulate tree growth response to future CO[sub 2]-induced climate change projected by GCMs. The comparable results of both models indicate that different conifer species have individualistic growth responses to future climatic change. The response behaviors of trees are affected greatly by local stand conditions. The results suggest possible changes in future growth and distributions of naturally occurring conifers in this region.

  6. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

    PubMed Central

    Szczecińska, Monika; Sawicki, Jakub

    2015-01-01

    Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and

  7. A comparison of spectral reflectance properties at the needle, branch, and canopy level for selected conifer species

    NASA Technical Reports Server (NTRS)

    Williams, Darrel L.

    1991-01-01

    Radiative transfer data were collected for three conifer species and a northern hardwood species. The data indicate that conifer forests are more absorptive than broadleaved, deciduous hardwood forests. In particular, spruce species have an enhanced capability of absorbing incoming solar radiation in the optical wavelength region.

  8. Exome capture from the spruce and pine giga-genomes.

    PubMed

    Suren, H; Hodgins, K A; Yeaman, S; Nurkowski, K A; Smets, P; Rieseberg, L H; Aitken, S N; Holliday, J A

    2016-09-01

    Sequence capture is a flexible tool for generating reduced representation libraries, particularly in species with massive genomes. We used an exome capture approach to sequence the gene space of two of the dominant species in Canadian boreal and montane forests - interior spruce (Picea glauca x engelmanii) and lodgepole pine (Pinus contorta). Transcriptome data generated with RNA-seq were coupled with draft genome sequences to design baits corresponding to 26 824 genes from pine and 28 649 genes from spruce. A total of 579 samples for spruce and 631 samples for pine were included, as well as two pine congeners and six spruce congeners. More than 50% of targeted regions were sequenced at >10× depth in each species, while ~12% captured near-target regions within 500 bp of a bait position were sequenced to a depth >10×. Much of our read data arose from off-target regions, which was likely due to the fragmented and incomplete nature of the draft genome assemblies. Capture in general was successful for the related species, suggesting that baits designed for a single species are likely to successfully capture sequences from congeners. From these data, we called approximately 10 million SNPs and INDELs in each species from coding regions, introns, untranslated and flanking regions, as well as from the intergenic space. Our study demonstrates the utility of sequence capture for resequencing in complex conifer genomes, suggests guidelines for improving capture efficiency and provides a rich resource of genetic variants for studies of selection and local adaptation in these species. PMID:27428061

  9. The problem of conifer species migration lag in the Pacific Northwest region since the last glaciation

    NASA Astrophysics Data System (ADS)

    Elias, Scott A.

    2013-10-01

    Multiproxy evidence indicates that warmer-than-present summers became established in Eastern Beringia as early as 14,000-13,000 years ago, but the dispersal of spruces, pines, cedars and hemlocks across the Pacific Northwest (PNW) region of southern Alaska did not begin until at least 1500 years afterwards, and took many thousands of years to be completed. There are many potential reasons for this slow spread of PNW conifers towards their modern range limits. The absence of mycorrhizae in the soils of southern Alaska may have slowed conifer establishment. The availability of soil moisture was another limiting factor. With the exception of Pinus contorta, the other PNW conifers become established most readily from seeds that fall on moist, shaded substrates, thus they are not good pioneering species. Competition with alder and birch played an important role, especially along Prince William Sound and the Kenai Peninsula. Alder or alder and birch dominated these regions until the mid- to late Holocene. The other key element for most PNW conifer species is the precipitation regime. The hemlocks, cedars and Sitka spruce are not drought-hardy. So although the PNW temperature regime may have been warm enough in early postglacial times to support the growth of PNW conifers, it was probably too dry for them to successfully become established in new regions. The conflation of these environmental factors limits our present understanding of the problem, but the recent trend of multi-proxy analysis in Quaternary paleoecology will certainly sharpen our reconstructions. Such proxies as conifer needle stomata and insect fossil remains hold significant promise.

  10. Three centuries of managing introduced conifers in South Africa: Benefits, impacts, changing perceptions and conflict resolution.

    PubMed

    van Wilgen, Brian W; Richardson, David M

    2012-09-15

    Alien conifers, mainly pines, have been planted in South Africa for a range of purposes for over 300 years. Formal plantations cover 660,000 ha of the country, and invasive stands of varying density occur on a further 2.9 million ha. These trees have brought many benefits but have also caused unintended problems. The management of alien conifers has evolved in response to emerging problems such as excessive water use by plantations of conifers, changing values and markets, and the realities of a new ecological order brought about by invasive alien conifers. This paper reviews the history of conifer introductions to South Africa, the benefits and impacts with which they are associated, and the ongoing and evolving research that has been conducted to inform their management. The South African approach has included taking courageous steps to address the problem of highly invasive species that are also an important commercial crop. These interventions have not, however, had the desired effect of both retaining benefits from formal plantations while simultaneously reversing the trend of growing impacts associated with self-sown invasive stands. We suggest that different approaches need to be considered, including the systematic phasing out of commercial forestry in zones where it delivers low returns, and the introduction of more effective, focussed and integrated, region-specific approaches to the management of invasive stands of conifers. These steps would deliver much improved economic outcomes by protecting valuable ecosystem services, but will require political commitment to policies that could be unpopular in certain sectors of society.

  11. Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

    PubMed Central

    Harr, Bettina; Karakoc, Emre; Neme, Rafik; Teschke, Meike; Pfeifle, Christine; Pezer, Željka; Babiker, Hiba; Linnenbrink, Miriam; Montero, Inka; Scavetta, Rick; Abai, Mohammad Reza; Molins, Marta Puente; Schlegel, Mathias; Ulrich, Rainer G.; Altmüller, Janine; Franitza, Marek; Büntge, Anna; Künzel, Sven; Tautz, Diethard

    2016-01-01

    Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory. PMID:27622383

  12. Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.

    PubMed

    Harr, Bettina; Karakoc, Emre; Neme, Rafik; Teschke, Meike; Pfeifle, Christine; Pezer, Željka; Babiker, Hiba; Linnenbrink, Miriam; Montero, Inka; Scavetta, Rick; Abai, Mohammad Reza; Molins, Marta Puente; Schlegel, Mathias; Ulrich, Rainer G; Altmüller, Janine; Franitza, Marek; Büntge, Anna; Künzel, Sven; Tautz, Diethard

    2016-01-01

    Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory. PMID:27622383

  13. Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.

    PubMed

    Harr, Bettina; Karakoc, Emre; Neme, Rafik; Teschke, Meike; Pfeifle, Christine; Pezer, Željka; Babiker, Hiba; Linnenbrink, Miriam; Montero, Inka; Scavetta, Rick; Abai, Mohammad Reza; Molins, Marta Puente; Schlegel, Mathias; Ulrich, Rainer G; Altmüller, Janine; Franitza, Marek; Büntge, Anna; Künzel, Sven; Tautz, Diethard

    2016-01-01

    Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory.

  14. EXPANSION OF PCR-BASED MARKER RESOURCES IN OAT BY SURVEYING GENOMIC-DERIVED SSRs FROM BARLEY AND WHEAT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Identifying simple sequence repeat (SSR) regions in crop genomes and amplifying them with specific primer sets have provided a relatively new generation of molecular markers for mapping projects. SSRs are advantageous to most of other markers because they are present in large numbers, are evenly d...

  15. A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A key feature of a gene's function is the variety of protein isoforms it encodes in a population. However, the genetic diversity in bovine whole genome databases tends to be underrepresented because these databases contain an abundance of sequence from the most influential sires. Our first aim was ...

  16. Detection of aspen-conifer forest mixes from LANDSAT digital data. [Utah-Idaho Bear River Range

    NASA Technical Reports Server (NTRS)

    Jaynes, R. A.; Merola, J. A.

    1982-01-01

    Aspen, conifer and mixed aspen/conifer forests were mapped for a 15-quadrangle study area in the Utah-Idaho Bear River Range using LANDSAT multispectral scanner data. Digital classification and statistical analysis of LANDSAT data allowed the identification of six groups of signatures which reflect different types of aspen/conifer forest mixing. Photo interpretations of the print symbols suggest that such classes are indicative of mid to late seral aspen forests. Digital print map overlays and acreage calculations were prepared for the study area quadrangles. Further field verification is needed to acquire additional information about the nature of the forests. Single date LANDSAT analysis should be a cost effective means to index aspen forests which are at least in the mid seral phase of conifer invasion. Since aspen canopies tend to obscure understory conifers for early seral forests, a second date analysis, using data taken when aspens are leafless, could provide information about early seral aspen forests.

  17. Detection of aspen/conifer forest mixes from multitemporal Landsat digital data. [Utah-Idaho Bear River Range

    NASA Technical Reports Server (NTRS)

    Merola, J. A.; Jaynes, R. A.; Harniss, R. O.

    1984-01-01

    Aspen, conifer and mixed aspen/conifer forests were mapped for a 15-quadrangle study area in the Utah-Idaho Bear River Range using Landsat multispectral scanner data. Digital classification and statistical analysis of Landsat data allowed the identification of six groups of signatures which reflect different types of aspen/conifer forest mixing. Photo interpretations of the print symbols suggest that such classes are indicative of mid to late seral aspen forests. Digital print map overlayes and acreage calculations were prepared for the study area quadrangles. Further field verification is needed to acquire additional information about the nature of the forests. Single data Landsat analysis should be a cost effective means to index aspen forests which are at least in the mid seral phase of conifer invasion. Since aspen canopies tend to obscure understory conifers for early seral forests, a second data analysis, using data taken when aspens are leafless, could provide information about early seral aspen forests.

  18. Evolution of conifer diterpene synthases: diterpene resin acid biosynthesis in lodgepole pine and jack pine involves monofunctional and bifunctional diterpene synthases.

    PubMed

    Hall, Dawn E; Zerbe, Philipp; Jancsik, Sharon; Quesada, Alfonso Lara; Dullat, Harpreet; Madilao, Lina L; Yuen, Macaire; Bohlmann, Jörg

    2013-02-01

    Diterpene resin acids (DRAs) are major components of pine (Pinus spp.) oleoresin. They play critical roles in conifer defense against insects and pathogens and as a renewable resource for industrial bioproducts. The core structures of DRAs are formed in secondary (i.e. specialized) metabolism via cycloisomerization of geranylgeranyl diphosphate (GGPP) by diterpene synthases (diTPSs). Previously described gymnosperm diTPSs of DRA biosynthesis are bifunctional enzymes that catalyze the initial bicyclization of GGPP followed by rearrangement of a (+)-copalyl diphosphate intermediate at two discrete class II and class I active sites. In contrast, similar diterpenes of gibberellin primary (i.e. general) metabolism are produced by the consecutive activity of two monofunctional class II and class I diTPSs. Using high-throughput transcriptome sequencing, we discovered 11 diTPS from jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta). Three of these were orthologous to known conifer bifunctional levopimaradiene/abietadiene synthases. Surprisingly, two sets of orthologous PbdiTPSs and PcdiTPSs were monofunctional class I enzymes that lacked functional class II active sites and converted (+)-copalyl diphosphate, but not GGPP, into isopimaradiene and pimaradiene as major products. Diterpene profiles and transcriptome sequences of lodgepole pine and jack pine are consistent with roles for these diTPSs in DRA biosynthesis. The monofunctional class I diTPSs of DRA biosynthesis form a new clade within the gymnosperm-specific TPS-d3 subfamily that evolved from bifunctional diTPS rather than monofunctional enzymes (TPS-c and TPS-e) of gibberellin metabolism. Homology modeling suggested alterations in the class I active site that may have contributed to their functional specialization relative to other conifer diTPSs. PMID:23370714

  19. Evolution of Conifer Diterpene Synthases: Diterpene Resin Acid Biosynthesis in Lodgepole Pine and Jack Pine Involves Monofunctional and Bifunctional Diterpene Synthases1[W][OA

    PubMed Central

    Hall, Dawn E.; Zerbe, Philipp; Jancsik, Sharon; Quesada, Alfonso Lara; Dullat, Harpreet; Madilao, Lina L.; Yuen, Macaire; Bohlmann, Jörg

    2013-01-01

    Diterpene resin acids (DRAs) are major components of pine (Pinus spp.) oleoresin. They play critical roles in conifer defense against insects and pathogens and as a renewable resource for industrial bioproducts. The core structures of DRAs are formed in secondary (i.e. specialized) metabolism via cycloisomerization of geranylgeranyl diphosphate (GGPP) by diterpene synthases (diTPSs). Previously described gymnosperm diTPSs of DRA biosynthesis are bifunctional enzymes that catalyze the initial bicyclization of GGPP followed by rearrangement of a (+)-copalyl diphosphate intermediate at two discrete class II and class I active sites. In contrast, similar diterpenes of gibberellin primary (i.e. general) metabolism are produced by the consecutive activity of two monofunctional class II and class I diTPSs. Using high-throughput transcriptome sequencing, we discovered 11 diTPS from jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta). Three of these were orthologous to known conifer bifunctional levopimaradiene/abietadiene synthases. Surprisingly, two sets of orthologous PbdiTPSs and PcdiTPSs were monofunctional class I enzymes that lacked functional class II active sites and converted (+)-copalyl diphosphate, but not GGPP, into isopimaradiene and pimaradiene as major products. Diterpene profiles and transcriptome sequences of lodgepole pine and jack pine are consistent with roles for these diTPSs in DRA biosynthesis. The monofunctional class I diTPSs of DRA biosynthesis form a new clade within the gymnosperm-specific TPS-d3 subfamily that evolved from bifunctional diTPS rather than monofunctional enzymes (TPS-c and TPS-e) of gibberellin metabolism. Homology modeling suggested alterations in the class I active site that may have contributed to their functional specialization relative to other conifer diTPSs. PMID:23370714

  20. The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

    PubMed Central

    Ernst, R.; Mayer, K. F. X.

    2004-01-01

    The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project. PMID:18629059

  1. Assessing Conifer Ray Parenchyma for Ecological Studies: Pitfalls and Guidelines

    PubMed Central

    von Arx, Georg; Arzac, Alberto; Olano, José M.; Fonti, Patrick

    2015-01-01

    provided the least accurate PERPAR estimates. This evaluation of ray parenchyma in conifers and the presented guidelines regarding data accuracy as a function of measured wood surface and number of samples represent an important methodological reference for ray quantification, which will ultimately improve the understanding of the fundamental role of ray parenchyma tissue for the performance and survival of trees growing in stressed environments. PMID:26635842

  2. Diagenesis of conifer needles in a coastal marine environment

    NASA Astrophysics Data System (ADS)

    Hedges, John I.; Weliky, K.

    1989-10-01

    (C/V) of the deepest sedimentary fir/hemlock needles to 20% of the original value and almost tripled the carbon-normalized yield of total vanillyl plus cinnamyl phenols (Λ). The net result of these compositional variations was to make the lignin component of the buried conifer needles resemble lignin in gymnosperm wood, thereby leading to underestimates of needle input and mass.

  3. Stem demography and postfire recruitment of a resprouting serotinous conifer

    USGS Publications Warehouse

    Keeley, Jon E.; Keeley, Melanie B.; Bond, William J.

    1999-01-01

    The contribution of resprouts and seedling recruitment to post-fire regeneration of the South African fynbos conifer Widdringtonia nodiflora was compared eight months after wildfires in 1990. Stems on all trees were killed by fire but resprouting success was > 90 % at all but one site. A demographic study of burned skeletons revealed that prior to these fires, nearly all plants were multi-stemmed (4–9 stems/plant) and multi-aged, indicating continuous sprout production between fires. All stems were killed by these 1990 fires and at most sites > 90 % of the stems were burned to ground level. All diameter stems were susceptible to such incineration as, at most sites, there was no difference in average diameter of stems burned to ground level and those left standing. Individual genets usually had all ramets incinerated to ground level or all ramets charred, but intact, suggesting certain micro-sites burned hotter, whereas other sites were somewhat protected. Although not true of the 1990 fires, there was evidence that occasionallyWiddring-tonia stems may survive fire. At one site, four of the 16 plants sampled had a burned stem twice as old as the oldest burned stem on the other 12 plants at the site, suggesting some stems had survived the previous fire (ca. 1970) and this conclusion was supported by fire-scars on these four stems that dated to ca. 1970. Based on the highly significant correlation between stem diameter and cone density left standing after the 1990 fires, we calculated that for most sites > 80 % of the initial cone crop was incinerated by fire. This is important because we observed a strong relationship between size of the canopy cone crop surviving fire and post-fire seedling recruitment. Under these conditions we hypothesize that sprouting confers a selective advantage to genets when fires cause heavy losses of seed. The infrequent occurrence of sprouting in theCupressaceae suggests the hypothesis that resprouting is an apomorphic or derived trait

  4. Assessing Conifer Ray Parenchyma for Ecological Studies: Pitfalls and Guidelines.

    PubMed

    von Arx, Georg; Arzac, Alberto; Olano, José M; Fonti, Patrick

    2015-01-01

    provided the least accurate PERPAR estimates. This evaluation of ray parenchyma in conifers and the presented guidelines regarding data accuracy as a function of measured wood surface and number of samples represent an important methodological reference for ray quantification, which will ultimately improve the understanding of the fundamental role of ray parenchyma tissue for the performance and survival of trees growing in stressed environments. PMID:26635842

  5. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction.

    PubMed

    Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A; Lyons, Russell E; Salin, Krishna R; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B

    2016-01-01

    The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. PMID:27164098

  6. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction.

    PubMed

    Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A; Lyons, Russell E; Salin, Krishna R; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B

    2016-05-07

    The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.

  7. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction

    PubMed Central

    Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A.; Lyons, Russell E.; Salin, Krishna R.; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B.

    2016-01-01

    The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. PMID:27164098

  8. Comparing growth phenology of co-occurring deciduous and evergreen conifers exposed to drought

    PubMed Central

    Swidrak, Irene; Schuster, Roman; Oberhuber, Walter

    2013-01-01

    Plant phenological events are influenced by climate factors such as temperature and rainfall. To evaluate phenological responses to water availability in a Spring Heath-Pine wood (Erico-Pinetum typicum), the focus of this study was to determine intra-annual dynamics of apical and lateral growth of co-occurring early successional Larix decidua and Pinus sylvestris and late successional Picea abies exposed to drought. The effect of reduced plant water availability on growth phenology was investigated by conducting a rainfall exclusion experiment. Timing of key phenological dates (onset, maximum rate, end, duration) of growth processes were compared among species at the rain-sheltered and control plot during 2011 and 2012. Shoot and needle elongation were monitored on lateral branches in the canopy at c. 16 m height and radial growth was recorded by automatic dendrometers at c. 1.3 m height of > 120 yr old trees. Different sequences in aboveground growth phenology were detected among the three species under the same growing conditions. While onset of radial growth in April through early May was considerably preceded by onset of needle growth in Larix decidua (5 - 6 weeks) and shoot growth in Pinus sylvestris (c. 3 weeks), it occurred quite simultaneously with onset of shoot growth in Picea abies. Low water availability had a minor impact on onset of aboveground growth, which is related to utilization of stored water, but caused premature cessation of aboveground growth. At the control plot mean growing season length was 130 days in Pinus sylvestris, 95 days in Larix decidua and 73 days in Picea abies supporting the hypothesis that early successional species are resource expenders, while late successional species are more efficient in utilizing resources and develop safer life strategies. High synchronicity found in culmination of radial growth in late spring (mid-May through early June) prior to occurrence of more favourable environmental conditions in summer might

  9. Comparing growth phenology of co-occurring deciduous and evergreen conifers exposed to drought.

    PubMed

    Swidrak, Irene; Schuster, Roman; Oberhuber, Walter

    2013-12-01

    Plant phenological events are influenced by climate factors such as temperature and rainfall. To evaluate phenological responses to water availability in a Spring Heath-Pine wood (Erico-Pinetum typicum), the focus of this study was to determine intra-annual dynamics of apical and lateral growth of co-occurring early successional Larix decidua and Pinus sylvestris and late successional Picea abies exposed to drought. The effect of reduced plant water availability on growth phenology was investigated by conducting a rainfall exclusion experiment. Timing of key phenological dates (onset, maximum rate, end, duration) of growth processes were compared among species at the rain-sheltered and control plot during 2011 and 2012. Shoot and needle elongation were monitored on lateral branches in the canopy at c. 16 m height and radial growth was recorded by automatic dendrometers at c. 1.3 m height of > 120 yr old trees. Different sequences in aboveground growth phenology were detected among the three species under the same growing conditions. While onset of radial growth in April through early May was considerably preceded by onset of needle growth in Larix decidua (5 - 6 weeks) and shoot growth in Pinus sylvestris (c. 3 weeks), it occurred quite simultaneously with onset of shoot growth in Picea abies. Low water availability had a minor impact on onset of aboveground growth, which is related to utilization of stored water, but caused premature cessation of aboveground growth. At the control plot mean growing season length was 130 days in Pinus sylvestris, 95 days in Larix decidua and 73 days in Picea abies supporting the hypothesis that early successional species are resource expenders, while late successional species are more efficient in utilizing resources and develop safer life strategies. High synchronicity found in culmination of radial growth in late spring (mid-May through early June) prior to occurrence of more favourable environmental conditions in summer might

  10. The impact of catchment conifer plantation forestry on the hydrochemistry of peatland lakes.

    PubMed

    Drinan, T J; Graham, C T; O'Halloran, J; Harrison, S S C

    2013-01-15

    The hydrochemistry of 26 small blanket bog lakes was examined to assess the impact of conifer plantation forestry on lake water chemistry. Lakes were selected from three distinct catchment land use categories: i) unplanted blanket bog only present in the catchment, ii) mature (closed-canopy) conifer plantation forests only present in the catchment and iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sedimentary (sandstone) and igneous (granite). Lakes with afforested catchments across both geologies had elevated concentrations of phosphorus (P), nitrogen (N), total dissolved organic carbon (TDOC), aluminium (Al) and iron (Fe), with the highest concentrations of each parameter recorded from lakes with catchment clearfelling. Dissolved oxygen was also significantly reduced in the afforested lakes, particularly the clearfell lakes. Analysis of runoff from a nearby recently clearfelled site revealed high biological and chemical oxygen demands, consistent with at least part of the elevated concentrations of TDOC emanating from clearfelled sites having higher biochemical lability. Inorganic fertilisers applied at the start of the forest cycle, the decay of the underlying peat soil and accumulated surface tree litter, and leachate from felled trees are the likely sources of the elevated concentrations of plant nutrients, TDOC, heavy metals and major ions, with excessive peat soil disturbance during clearfelling likely exacerbating the runoff into lakes. Our study has demonstrated a clear, deleterious impact of conifer plantations on the water quality draining from blanket bog catchments, with major implications for the management of afforested peatlands.

  11. Response of conifer-encroached shrublands in the Great Basin to prescribed fire and mechanical treatments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In response to the recent expansion of piñon and juniper woodlands into sagebrush steppe communities in the northern Great Basin region, numerous conifer removal projects have been implemented at sites having a wide range of environmental conditions. Response has varied from successful restoration t...

  12. Repeated freeze-thaw cycles induce embolism in drought stressed conifers (Norway spruce, stone pine).

    PubMed

    Mayr, Stefan; Gruber, Andreas; Bauer, Helmut

    2003-07-01

    Freezing and thawing lead to xylem embolism when gas bubbles caused by ice formation expand during the thaw process. However, previous experimental studies indicated that conifers are resistant to freezing-induced embolism, unless xylem pressure becomes very negative during the freezing. In this study, we show that conifers experienced freezing-induced embolism when exposed to repeated freeze-thaw cycles and simultaneously to drought. Simulating conditions at the alpine timberline (128 days with freeze-thaw events and thawing rates of up to 9.5 K h(-1) in the xylem of exposed twigs during winter), young trees of Norway spruce [Picea abies (L.) Karst.] and stone pine (Pinus cembra L.) were exposed to 50 and 100 freeze-thaw cycles. This treatment caused a significant increase in embolism rates in drought-stressed samples. Upon 100 freeze-thaw cycles, vulnerability thresholds (50% loss of conductivity) were shifted 1.8 MPa (Norway spruce) and 0.8 MPa (stone pine) towards less negative water potentials. The results demonstrate that freeze-thaw cycles are a possible reason for winter-embolism in conifers observed in several field studies. Freezing-induced embolism may contribute to the altitudinal limits of conifers.

  13. The sage-grouse habitat mortgage: effective conifer management in space and time

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Management of conservation-reliant species can be complicated by the need to manage ecosystem processes that operate at extended temporal horizons. One such process is the role of fire in regulating abundance of expanding conifers that disrupt sage-grouse habitat in the northern Great Basin of the ...

  14. Impact of conifer forest litter on microwave emission at L-band

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study reports on the utilization of microwave modeling, together with ground truth and L-bank (1.4 GHz) brightness temperatures to investigate the characteristics of conifer forest floor. The microwave data were acquired over natural Virginia pine forest in Maryland by ComRAD, a ground-based mi...

  15. Bird communities associated with succession and management of lowland conifer forests

    USGS Publications Warehouse

    Dawson, D.K.

    1979-01-01

    Data from published bird censuses were used to determine changes in avian communities in relation to plant succession, fire, type conversion, and timber management practices in lowland conifer forests in the northeastern United States. With modifications in current logging practices, habitat for the bird species that nest in undisturbed stands can be provided. Management guidelines are recommended.

  16. In vivo 13C NMR metabolite profiling: potential for understanding and assessing conifer seed quality.

    PubMed

    Terskikh, Victor V; Feurtado, J Allan; Borchardt, Shane; Giblin, Michael; Abrams, Suzanne R; Kermode, Allison R

    2005-08-01

    High-resolution 13C MAS NMR spectroscopy was used to profile a range of primary and secondary metabolites in vivo in intact whole seeds of eight different conifer species native to North America, including six of the Pinaceae family and two of the Cupressaceae family. In vivo 13C NMR provided information on the total seed oil content and fatty acid composition of the major storage lipids in a non-destructive manner. In addition, a number of monoterpenes were identified in the 13C NMR spectra of conifer seeds containing oleoresin; these compounds showed marked variability in individual seeds of Pacific silver fir within the same seed lot. In imbibed conifer seeds, the 13C NMR spectra showed the presence of considerable amounts of dissolved sucrose presumed to play a protective role in the desiccation-tolerance of seeds. The free amino acids arginine and asparagine, generated as a result of storage protein mobilization, were detected in vivo during seed germination and early seedling growth. The potential for NMR to profile metabolites in a non-destructive manner in single conifer seeds and seed populations is discussed. It is a powerful tool to evaluate seed quality because of its ability to assess reserve accumulation during seed development or at seed maturity; it can also be used to monitor reserve mobilization, which is critical for seedling emergence. PMID:15996983

  17. Antifungal activity of extracts and select compounds in heartwood of seven western conifers toward Phytophthora ramorum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Individual compounds and ethyl acetate extracts from heartwood of seven conifer species were tested for fungicidal activity against Phytophthora ramorum. Extracts from incense and western red cedar exhibited the strongest activity (EC50 589 and 646 ppm, respectively), yellow-cedar, western juniper,...

  18. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  19. Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Culicoides biting midges (Diptera: Ceratopogonidae) are a major vector group responsible for the biological transmission of a wide variety of globally significant arboviruses, including bluetongue virus (BTV). In this review we examine current biological resources for the study of this genus, with a...

  20. Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: A genomic resource for studying agricultural pests

    PubMed Central

    Noda, Hiroaki; Kawai, Sawako; Koizumi, Yoko; Matsui, Kageaki; Zhang, Qiang; Furukawa, Shigetoyo; Shimomura, Michihiko; Mita, Kazuei

    2008-01-01

    Background The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background. Results More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site. Conclusion The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest. PMID:18315884

  1. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

    PubMed

    Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H

    2015-07-01

    Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.

  2. Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.

    PubMed

    Lees, Jonathan; Yeats, Corin; Perkins, James; Sillitoe, Ian; Rentzsch, Robert; Dessailly, Benoit H; Orengo, Christine

    2012-01-01

    Gene3D http://gene3d.biochem.ucl.ac.uk is a comprehensive database of protein domain assignments for sequences from the major sequence databases. Domains are directly mapped from structures in the CATH database or predicted using a library of representative profile HMMs derived from CATH superfamilies. As previously described, Gene3D integrates many other protein family and function databases. These facilitate complex associations of molecular function, structure and evolution. Gene3D now includes a domain functional family (FunFam) level below the homologous superfamily level assignments. Additions have also been made to the interaction data. More significantly, to help with the visualization and interpretation of multi-genome scale data sets, we have developed a new, revamped website. Searching has been simplified with more sophisticated filtering of results, along with new tools based on Cytoscape Web, for visualizing protein-protein interaction networks, differences in domain composition between genomes and the taxonomic distribution of individual superfamilies.

  3. Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach.

    PubMed

    Knies, David; Wittmüß, Philipp; Appel, Sebastian; Sawodny, Oliver; Ederer, Michael; Feuer, Ronny

    2015-01-01

    The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data. PMID:26516924

  4. Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach

    PubMed Central

    Knies, David; Wittmüß, Philipp; Appel, Sebastian; Sawodny, Oliver; Ederer, Michael; Feuer, Ronny

    2015-01-01

    The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data. PMID:26516924

  5. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    PubMed Central

    Cerdà, Joan; Mercadé, Jaume; Lozano, Juan José; Manchado, Manuel; Tingaud-Sequeira, Angèle; Astola, Antonio; Infante, Carlos; Halm, Silke; Viñas, Jordi; Castellana, Barbara; Asensio, Esther; Cañavate, Pedro; Martínez-Rodríguez, Gonzalo; Piferrer, Francesc; Planas, Josep V; Prat, Francesc; Yúfera, Manuel; Durany, Olga; Subirada, Francesc; Rosell, Elisabet; Maes, Tamara

    2008-01-01

    Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions. PMID:18973667

  6. Molecular genomics resource for the parasitic nematode Spirocerca lupi: Identification of 149 microsatellite loci using FIASCO and next generation sequencing.

    PubMed

    Reid, Kerry; Mitha, Janishtha R; Greeff, Jaco M; de Waal, Pamela J

    2015-01-01

    Understanding genetic diversity and movement patterns in parasitic organisms is paramount to establish control and management strategies. In this study we developed a microsatellite resource as well as a diagnostic multiplex for the cosmopolitan parasitic nematode Spirocerca lupi, known to cause spirocercosis in canids. A combination of microsatellite enrichment and 454 sequencing was used to identify 149 unique microsatellite loci in S. lupi. Twenty loci were characterized further in two sampling sites in South Africa, with 10 loci identified as polymorphic (allele ranges from 4 to 17). These loci were designed into a single diagnostic multiplex suitable for species identification and population genetics studies. The markers were also successful in cross-species amplification in Cylicospirura felineus, Philonema oncorhynchi and Gongylonema pulchrum. Our resource provides a large set of candidate loci for a number of nematode studies as well as loci suitable for diversity and population genetics studies of S. lupi within the South African context as well as globally.

  7. Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish

    PubMed Central

    Spivakov, Mikhail; Auer, Thomas O.; Peravali, Ravindra; Dunham, Ian; Dolle, Dirk; Fujiyama, Asao; Toyoda, Atsushi; Aizu, Tomoyuki; Minakuchi, Yohei; Loosli, Felix; Naruse, Kiyoshi; Birney, Ewan; Wittbrodt, Joachim

    2014-01-01

    Oryzias latipes (medaka) has been established as a vertebrate genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel. PMID:24408034

  8. A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)

    PubMed Central

    2013-01-01

    Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single

  9. Investigating the impacts of recycled water on long-lived conifers

    PubMed Central

    Nackley, Lloyd L.; Barnes, Corey; Oki, Lorence R.

    2015-01-01

    Recycled wastewater is a popular alternative water resource. Recycled water typically has higher salinity than potable water and therefore may not be an appropriate water source for landscapes planted with salt-intolerant plant species. Coast redwoods (Sequoia sempervirens) are an important agricultural, horticultural and ecological species assumed to be salt intolerant. However, no studies have analysed how salinity impacts coast redwood growth. To determine salt-related growth limitations, as well as susceptibility to particular salt ions, we divided 102 S. sempervirens ‘Aptos Blue’ saplings evenly into 17 salinity treatments: a control and four different salts (sodium chloride, calcium chloride, sodium chloride combined with calcium chloride, and sodium sulfate). Each salt type was applied at four different concentrations: 1.0, 3.0, 4.5 and 6.0 dS m−1. Trees were measured for relative growth, and leaves were analysed for ion accumulation. Results showed that the relative stem diameter growth was inversely proportional to the increase in salinity (electrical conductivity), with R2 values ranging from 0.72 to 0.82 for different salts. Analysis of variance tests indicated that no particular salt ion significantly affected growth differently than the others (P > 0.1). Pairwise comparisons of the means revealed that moderately saline soils (4–8 dS m−1) would decrease the relative height growth by 30–40 %. Leaf tissue analysis showed that all treatment groups accumulated salt ions. This finding suggests reduced growth and leaf burn even at the lowest ion concentrations if salts are not periodically leached from the soil. Regardless of the specific ions in the irrigation water, the results suggest that growth and appearance of coast redwoods will be negatively impacted when recycled water electrical conductivity exceeds >1.0 dS m−1. This information will prove valuable to many metropolitan areas faced with conserving water while at the same time

  10. Leaf wax composition and carbon isotopes vary among major conifer groups

    NASA Astrophysics Data System (ADS)

    Diefendorf, Aaron F.; Leslie, Andrew B.; Wing, Scott L.

    2015-12-01

    Leaf waxes (e.g. n-alkanes, n-alkanoic acids) and their carbon isotopes (δ13C) are commonly used to track past changes in the carbon cycle, water availability, and plant ecophysiology. Previous studies indicated that conifers have lower n-alkane concentrations than angiosperms and that 13C fractionation during n-alkane synthesis (εn-alkane) is smaller than in angiosperms. These prior studies, however, sampled a limited phylogenetic and geographic subset of conifers, leaving out many important subtropical and Southern Hemisphere groups that were once widespread and common components of fossil assemblages. To expand on previous work, we collected 43 conifer species (and Ginkgo biloba) from the University of California Botanical Garden at Berkeley, sampling all extant conifer families and almost two-thirds of extant genera. We find that Pinaceae, including many North American species used in previous studies, have very low or no n-alkanes. However, other conifer groups have significant concentrations of n-alkanes, especially Southern Hemisphere Araucariaceae and Podocarpaceae (monkey puzzles, Norfolk Island pines, and yellowwoods), and many species of Cupressaceae (junipers and relatives). Within the Cupressaceae, we find total n-alkane concentrations are high in subfamilies Cupressoideae and Callitroideae, but significantly lower in the early diverging taxodioid lineages (including bald cypress and redwood). Individual n-alkane chain lengths have a weak phylogenetic signal, except for n-C29 alkane, but when combined using average chain length (ACL), a strong phylogenetic signal emerges. The strong phylogenetic signal in ACL, observed in the context of a common growth environment for all plants we sampled, suggests that ACL is strongly influenced by factors other than climate. An analysis of εn-alkane indicates a strong phylogenetic signal in which the smallest biosynthetic fractionation occurs in Pinaceae and the largest in Taxaceae (yews and relatives). The

  11. Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.

    PubMed

    Harris, Stephen E; O'Neill, Rachel J; Munshi-South, Jason

    2015-03-01

    Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of nonmodel species. We utilized two next-generation sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low-coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby and assembled a reference transcriptome using 1 080 065 954 SOLiD 5500XL (75 bp) reads and 3 052 640 454 GS FLX + reads. The reference contained 40 908 contigs with a N50 = 1044 bp and a total content of 30.06 Megabases (Mb). Contigs were annotated from Mus musculus (39.96% annotated) Uniprot databases. We identified 104 655 high-quality single nucleotide polymorphisms (SNPs) and 65 single sequence repeats (SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation. PMID:24980186

  12. Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.

    PubMed

    Harris, Stephen E; O'Neill, Rachel J; Munshi-South, Jason

    2015-03-01

    Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of nonmodel species. We utilized two next-generation sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low-coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby and assembled a reference transcriptome using 1 080 065 954 SOLiD 5500XL (75 bp) reads and 3 052 640 454 GS FLX + reads. The reference contained 40 908 contigs with a N50 = 1044 bp and a total content of 30.06 Megabases (Mb). Contigs were annotated from Mus musculus (39.96% annotated) Uniprot databases. We identified 104 655 high-quality single nucleotide polymorphisms (SNPs) and 65 single sequence repeats (SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation.

  13. IDENTIFICATION AND EMISSION FACTORS OF MOLECULAR TRACERS IN ORGANIC AEROSOLS FROM BIOMASS BURNING PART 1. TEMPERATE CLIMATE CONIFERS. (R823990)

    EPA Science Inventory

    Smoke particulate matter from conifers subjected to controlled burning, both under smoldering and flaming conditions, was sampled by high volume air filtration on precleaned quartz fiber filters. The filtered particles were extracted with dichloromethane and the crude extracts...

  14. Determination of variability in leaf biomass densities of conifers and mixed conifers under different environmental conditions in the San Joaquin Valley air basin. Final report

    SciTech Connect

    Temple, P.J.; Mutters, R.J.; Adams, C.; Greene, J.; Jackson, R.

    1995-06-01

    Biomass sampling plots were established at 29 locations within the dominant vegetation zones of the study area. Estimates of foliar biomass were made for each plot by three independent methods: regression analysis on the basis of tree diameter, calculation of the amount of light intercepted by the leaf canopy, and extrapolation from branch leaf area. Multivariate regression analysis was used to relate these foliar biomass estimates for oak plots and conifer plots to several independent predictor variables, including elevation, slope, aspect, temperature, precipitation, and soil chemical characteristics.

  15. Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

    PubMed Central

    Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

    2010-01-01

    The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

  16. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana).

    PubMed

    Pavy, Nathalie; Gagnon, France; Deschênes, Astrid; Boyle, Brian; Beaulieu, Jean; Bousquet, Jean

    2016-03-01

    Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.

  17. Hydraulic safety margins and embolism reversal in stems and leaves: why are conifers and angiosperms so different?

    PubMed

    Johnson, Daniel M; McCulloh, Katherine A; Woodruff, David R; Meinzer, Frederick C

    2012-10-01

    Angiosperm and coniferous tree species utilize a continuum of hydraulic strategies. Hydraulic safety margins (defined as differences between naturally occurring xylem pressures and pressures that would cause hydraulic dysfunction, or differences between pressures resulting in loss of hydraulic function in adjacent organs (e.g., stems vs. leaves) tend to be much greater in conifers than angiosperms and serve to prevent stem embolism. However, conifers tend to experience embolism more frequently in leaves and roots than angiosperms. Embolism repair is thought to occur by active transport of sugars into empty conduits followed by passive water movement. The most likely source of sugar for refilling is from nonstructural carbohydrate depolymerization in nearby parenchyma cells. Compared to angiosperms, conifers tend to have little parenchyma or nonstructural carbohydrates in their wood. The ability to rapidly repair embolisms may rely on having nearby parenchyma cells, which could explain the need for greater safety margins in conifer wood as compared to angiosperms. The frequent embolisms that occur in the distal portions of conifers are readily repaired, perhaps due to the abundant parenchyma in leaves and roots, and these distal tissues may act as hydraulic circuit breakers that prevent tension-induced embolisms in the attached stems. Frequent embolisms in conifer leaves may also be due to weaker stomatal response to changes in ambient humidity. Although there is a continuum of hydraulic strategies among woody plants, there appear to be two distinct 'behaviors' at the extremes: (1) embolism prevention and (2) embolism occurrence and subsequent repair.

  18. Hydraulic safety margins and embolism reversal in stems and leaves: why are conifers and angiosperms so different?

    PubMed

    Johnson, Daniel M; McCulloh, Katherine A; Woodruff, David R; Meinzer, Frederick C

    2012-10-01

    Angiosperm and coniferous tree species utilize a continuum of hydraulic strategies. Hydraulic safety margins (defined as differences between naturally occurring xylem pressures and pressures that would cause hydraulic dysfunction, or differences between pressures resulting in loss of hydraulic function in adjacent organs (e.g., stems vs. leaves) tend to be much greater in conifers than angiosperms and serve to prevent stem embolism. However, conifers tend to experience embolism more frequently in leaves and roots than angiosperms. Embolism repair is thought to occur by active transport of sugars into empty conduits followed by passive water movement. The most likely source of sugar for refilling is from nonstructural carbohydrate depolymerization in nearby parenchyma cells. Compared to angiosperms, conifers tend to have little parenchyma or nonstructural carbohydrates in their wood. The ability to rapidly repair embolisms may rely on having nearby parenchyma cells, which could explain the need for greater safety margins in conifer wood as compared to angiosperms. The frequent embolisms that occur in the distal portions of conifers are readily repaired, perhaps due to the abundant parenchyma in leaves and roots, and these distal tissues may act as hydraulic circuit breakers that prevent tension-induced embolisms in the attached stems. Frequent embolisms in conifer leaves may also be due to weaker stomatal response to changes in ambient humidity. Although there is a continuum of hydraulic strategies among woody plants, there appear to be two distinct 'behaviors' at the extremes: (1) embolism prevention and (2) embolism occurrence and subsequent repair. PMID:22920998

  19. A comparative field study of growth and survival of Sierran conifer seedlings

    SciTech Connect

    Kern, R.A.

    1996-12-31

    This study is a comparison of seedling growth and survival of seven species of conifers that make up the mid-elevation Sierra Nevada mixed conifer forest--Abies concolor, Abies magnifica, Calocedrus decurrens, Pinus jeffreyi, Pinus lambertiana, Pinus ponderosa, and Sequoiadendron giganteum. The field experiment was designed to test the hypothesis that seedling demography is affected by the study species` relatively shade and drought tolerances. Six discrete treatments were created in the first experiment by using three elevations (1,600 m, 1,900, m, and 2,200 m) and two natural light levels (closed canopy shade and open gap sun) at each elevation. One or two-year old seedlings were planted in the ground in replicate plots in each treatment and followed for two growing seasons. Four responses were analyzed--survival, height growth, diameter growth, and mass growth (total mass as well as root mass and shoot mass separately).

  20. Nutrient leaching from conifer needles in relation to foliar apoplast cation-exchange capacity

    SciTech Connect

    Turner, D.P.; van Broekhuizen, H.J.

    1992-01-01

    Limited evidence to date suggests that acidic precipitation promotes leaching of nutrient cations from conifer foliage. In order to evaluate the relative contribution of the apoplast cation exchange complex and symplast nutrient pools to the leached ions, the magnitude of potential foliar leaching in response to acidic precipitation was compared to foliar apoplast cation exchange capacity (CEC) for two conifer tree species (Pseudotsuga menziesii and Picea engelmanii). Leaching increased with decreasing pH and increasing time of immersion. At pH 2.1 and 3.1, equivalents of H+ depleted from the acidic solutions approximated equivalent of cations gained by the solutions. Maximum amounts leached were less than 40 micro equiv/g dry weight of needles for all ions combined. Measured foliar apoplast CEC for these species was approximately 120 micro equiv/g dry weight of needles. These relative magnitudes indicated that the apoplast provided the leached ions.

  1. Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae.

    PubMed

    Hajibabaei, Mehrdad; Xia, Junnan; Drouin, Guy

    2006-07-01

    The phylogenetic position of gnetophytes has long been controversial. We sequenced parts of the genes coding for the largest subunit of nuclear RNA polymerase I, II, and III and combined these sequences with those of four chloroplast genes, two mitochondrial genes, and 18S rRNA genes to address this issue. Both maximum likelihood and maximum parsimony analyses of the sites not affected by high substitution levels strongly support a phylogeny where gymnosperms and angiosperms are monophyletic, where cycads are at the base of gymnosperm tree and are followed by ginkgos, and where gnetophytes are grouped within conifers as the sister group of pines. The evolution of several morphological and molecular characters of gnetophytes and conifers will therefore need to be reinterpreted. PMID:16621615

  2. Fine root dynamics and forest production across a calcium gradient in northern hardwood and conifer ecosystems

    USGS Publications Warehouse

    Park, B.B.; Yanai, R.D.; Fahey, T.J.; Bailey, S.W.; Siccama, T.G.; Shanley, J.B.; Cleavitt, N.L.

    2008-01-01

    Losses of soil base cations due to acid rain have been implicated in declines of red spruce and sugar maple in the northeastern USA. We studied fine root and aboveground biomass and production in five northern hardwood and three conifer stands differing in soil Ca status at Sleepers River, VT; Hubbard Brook, NH; and Cone Pond, NH. Neither aboveground biomass and production nor belowground biomass were related to soil Ca or Ca:Al ratios across this gradient. Hardwood stands had 37% higher aboveground biomass (P = 0.03) and 44% higher leaf litter production (P < 0.01) than the conifer stands, on average. Fine root biomass (<2 mm in diameter) in the upper 35 cm of the soil, including the forest floor, was very similar in hardwoods and conifers (5.92 and 5.93 Mg ha-1). The turnover coefficient (TC) of fine roots smaller than 1 mm ranged from 0.62 to 1.86 y-1 and increased significantly with soil exchangeable Ca (P = 0.03). As a result, calculated fine root production was clearly higher in sites with higher soil Ca (P = 0.02). Fine root production (biomass times turnover) ranged from 1.2 to 3.7 Mg ha-1 y-1 for hardwood stands and from 0.9 to 2.3 Mg ha-1 y -1 for conifer stands. The relationship we observed between soil Ca availability and root production suggests that cation depletion might lead to reduced carbon allocation to roots in these ecosystems. ?? 2008 Springer Science+Business Media, LLC.

  3. A Water Budget Approach to Study the Hydrologic Response of Mountain Meadow Restoration Following Conifer Removal

    NASA Astrophysics Data System (ADS)

    Van Oosbree, G. F.; Surfleet, C. G.; Jasbinsek, J. J.

    2014-12-01

    Mountain meadows are important ecological habitats that have degraded in quality and distribution due to fire suppression and poor land use practices in the Sierra Nevada Mountains. Conifer encroachment in mountain meadows has accelerated and is one of the reasons for the decline of meadow habitat. To date there are few studies which quantify the hydrologic response of meadow restoration due to vegetation or conifer removal. This study is using a before after control intervention (BACI) study design to determine the hydrologic response of restoration to a historic meadow encroached by conifers (study meadow). A water budget approach has been developed to quantify the hydrology of the control and study meadow before and after restoration. Measurements of groundwater depth and soil moisture are currently being taken on the control and study meadows. A total of 14 Odyssey water level capacitance instruments were installed to a 1.5 meter depth and 14 soil moisture instruments were installed to a 30 cm depth using a spatially balanced random sampling approach. Electrical resistivity imaging (ERI) was used to determine soil moisture and depth to groundwater across forest-meadow ecotones present on the meadows. Additionally, ERI was used to extrapolate point measurements of groundwater depth and soil moisture across the study and control areas. The weekly water budget indicates differences between the control meadow and study meadow in the first year prior to conifer removal. The ERI indicated differences in sub surface geology, soil moisture, and groundwater depth both between the control and study meadows and along the forest-meadow ecotones. ERI was demonstrated to improve the spatial extrapolation of soil moisture and groundwater point measurements.

  4. Agroforestry: Conifers. (Latest citations from the Cab Abstracts database). NewSearch

    SciTech Connect

    Not Available

    1994-10-01

    The bibliography contains citations concerning the use of lands forested with conifers for crop and livestock production. Citations cover the grazing of livestock and the production of crops, including tomatoes, soybeans, lespedeza, wheat, rape, taro, cotton, cabbages, ginger, watermelons, and strawberries. Livestock discussed include cattle, sheep, geese, and horses. Economic analyses and economic models are presented. (Contains a minimum of 147 citations and includes a subject term index and title list.)

  5. Cone selection by Eurasian red squirrels in mixed conifer forests in the Italian Alps

    NASA Astrophysics Data System (ADS)

    Molinari, A.; Wauters, L. A.; Airoldi, G.; Cerinotti, F.; Martinoli, A.; Tosi, G.

    2006-07-01

    Tree squirrels are arboreal granivores that harvest and consume tree seeds both prior to and after seed-dispersal. Inter- and intraspecific patterns of seed predation suggest that squirrels may exert strong selective pressure on cone morphology and patterns of cone production, and suggest coevolutionary interactions between squirrels and conifers. In some pine species (genus Pinus), mutualistic relationships have evolved between cone (seed) traits and seed-dispersal behaviour by birds and rodents. In other species, feeding by seed predators has selected for cone traits that decrease intensity of seed consumption. In mixed conifer forests, red squirrels ( Sciurus vulgaris) feed intensively in some (target) trees but avoid others (nontarget trees). Here we explore defensive cone traits and seed traits correlated with tree selection for conifer species with different seed-dispersal strategies. No selection for cone traits existed in Pinus cembra, which has large wingless seeds, dispersed by birds and rodents. In Picea abies, the most favoured species, target trees had cones with more seeds per cone than nontarget trees, and number of seeds increased with cone length. Cone selection was most pronounced in Pinus sylvestris, where target trees had bigger cones with more seeds and higher total seed mass than nontarget trees. However, ratio of seed mass on cone mass did not differ among target and nontarget trees, suggesting that bigger cones also had more protective tissue, probably increasing difficulties for seed predators to gain access to seeds. Our results suggest that cone and seed traits of P. cembra facilitate seed consumption by squirrels, but that defensive cone traits of small-seeded conifers, in combination with annual differences in seed production (masting), might be the result of coevolution with seed-eating squirrels.

  6. Biomolecules preserved in ca. 168 million year old fossil conifer wood

    NASA Astrophysics Data System (ADS)

    Marynowski, Leszek; Otto, Angelika; Zatoń, Michał; Philippe, Marc; Simoneit, Bernd R. T.

    2007-03-01

    Biomarkers are widely known to occur in the fossil record, but the unaltered biomolecules are rarely reported from sediments older than Paleogene. Polar terpenoids, the natural products most resistant to degradation processes, were reported mainly from the Tertiary conifers, and the oldest known are Cretaceous in age. In this paper, we report the occurrence of relatively high concentrations of ferruginol derivatives and other polar diterpenoids, as well as their diagenetic products, in a conifer wood Protopodocarpoxylon from the Middle Jurassic of Poland. Thus, the natural product terpenoids reported in this paper are definitely the oldest polar biomolecules detected in geological samples. The extracted phenolic abietanes like ferruginol and its derivatives (6,7-dehydroferruginol, sugiol, 11,14-dioxopisiferic acid) are produced only by distinct conifer families (Cupressaceae s. l., Podocarpaceae and Araucariaceae), to which Protopodocarpoxylon could belong based on anatomical characteristics. Therefore, the natural product terpenoids are of great advantage in systematics of fossil plant remains older than Paleogene and lacking suitable anatomical preservation.

  7. Electrodeposited Nanolaminated CoNiFe Cores for Ultracompact DC-DC Power Conversion

    SciTech Connect

    Kim, J; Kim, M; Herrault, F; Park, JY; Allen, MG

    2015-09-01

    Laminated metallic alloy cores (i.e., alternating layers of thin film metallic alloy and insulating material) of appropriate lamination thickness enable suppression of eddy current losses at high frequencies. Magnetic cores comprised of many such laminations yield substantial overall magnetic volume, thereby enabling high-power operation. Previously, we reported nanolaminated permalloy (Ni-80 Fe-20) cores based on a sequential electrodeposition technique, demonstrating negligible eddy current losses at peak flux densities up to 0.5 T and operating at megahertz frequencies. This paper demonstrates improved performance of nanolaminated cores comprising tens to hundreds of layers of 300-500-nm-thick CoNiFe films that exhibit superior magnetic properties (e.g., higher saturation flux density and lower coercivity) than permalloy. Nanolaminated CoNiFe cores can be operated up to a peak flux density of 0.9 T, demonstrating improved power handling capacity and exhibiting 30% reduced volumetric core loss, attributed to lowered hysteresis losses compared to the nanolaminated permalloy core of the same geometry. Operating these cores in a buck dc-dc power converter at a switching frequency of 1 MHz, the nanolaminated CoNiFe cores achieved a conversion efficiency exceeding 90% at output power levels up to 7 W, compared to an achieved permalloy core conversion efficiency below 86% at 6 W.

  8. A comparative study of modern and fossil cone scales and seeds of conifers: A geochemical approach

    USGS Publications Warehouse

    Artur, Stankiewicz B.; Mastalerz, Maria; Kruge, M.A.; Van Bergen, P. F.; Sadowska, A.

    1997-01-01

    Modern cone scales and seeds of Pinus strobus and Sequoia sempervirens, and their fossil (Upper Miocene, c. 6 Mar) counterparts Pinus leitzii and Sequoia langsdorfi have been studied using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), electron-microprobe and scanning electron microscopy. Microscopic observations revealed only minor microbial activity and high-quality structural preservation of the fossil material. The pyrolysates of both modern genera showed the presence of ligno-cellulose characteristic of conifers. However, the abundance of (alkylated)phenols and 1,2-benzenediols in modern S. sempervirens suggests the presence of non-hydrolysable tannins or abundant polyphenolic moieties not previously reported in modern conifers. The marked differences between the pyrolysis products of both modern genera are suggested to be of chemosystematic significance. The fossil samples also contained ligno-cellulose which exhibited only partial degradation, primarily of the carbohydrate constituents. Comparison between the fossil cone scale and seed pyrolysates indicated that the ligno-cellulose complex present in the seeds is chemically more resistant than that in the cone scales. Principal component analysis (PCA) of the pyrolysis data allowed for the determination of the discriminant functions used to assess the extent of degradation and the chemosystematic differences between both genera and between cone scales and seeds. Elemental composition (C, O, S), obtained using electron-microprobe, corroborated the pyrolysis results. Overall, the combination of chemical, microscopic and statistical methods allowed for a detailed characterization and chemosystematic interpretations of modern and fossil conifer cone scales and seeds.

  9. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

    PubMed Central

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-01-01

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program. PMID:26540077

  10. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement.

    PubMed

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-11-02

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.

  11. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement.

    PubMed

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-01-01

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program. PMID:26540077

  12. Oviposition strategies of conifer seed chalcids in relation to host phenology.

    PubMed

    Rouault, Gaëlle; Turgeon, Jean; Candau, Jean-Noël; Roques, Alain; von Aderkas, Patrick

    2004-10-01

    Insects are considered the most important predators of seed cones, the female reproductive structures of conifers, prior to seed dispersal. Slightly more than 100 genera of insects are known to parasitize conifer seed cones. The most diverse (i.e., number of species) of these genera is Megastigmus (Hymenoptera: Torymidae), which comprises many important seed pests of native and exotic conifers. Seed chalcids, Megastigmus spp., lay eggs inside the developing ovules of host conifers and, until recently, oviposition was believed to occur only in fertilized ovules. Ovule development begins just after pollination, but stops if cells are not fertilized. The morphological stage of cone development at the time of oviposition by seed chalcids has been established for many species; however, knowledge of ovule development at that time has been documented for only one species, M. spermotrophus. Megastigmus spermotrophus oviposits in Douglas-fir ovules after pollination but before fertilization. Unlike the unfertilized ovules, those containing a M. spermotrophus larva continue to develop, whether fertilized or not, stressing the need to broaden our understanding of the insect-plant interactions for this entire genus. To achieve this task, we reviewed the scientific literature and assembled information pertaining to the timing of oviposition and to the pollination and fertilization periods of their respective host(s). More specifically, we were searching for circumstantial evidence that other species of Megastigmus associated with conifers could behave (i.e., oviposit before ovule fertilization) and impact on female gametophyte (i.e., prevent abortion) like M. spermotrophus. The evidence from our compilation suggests that seed chalcids infesting Pinaceae may also oviposit before ovule fertilization, just like M. spermotrophus, whereas those infesting Cupressaceae seemingly oviposit after ovule fertilization. Based on this evidence, we hypothesize that all species of Megastigmus

  13. Oviposition strategies of conifer seed chalcids in relation to host phenology

    NASA Astrophysics Data System (ADS)

    Rouault, Gaëlle; Turgeon, Jean; Candau, Jean-Noël; Roques, Alain; Aderkas, Patrick

    2004-10-01

    Insects are considered the most important predators of seed cones, the female reproductive structures of conifers, prior to seed dispersal. Slightly more than 100 genera of insects are known to parasitize conifer seed cones. The most diverse (i.e., number of species) of these genera is Megastigmus (Hymenoptera: Torymidae), which comprises many important seed pests of native and exotic conifers. Seed chalcids, Megastigmus spp., lay eggs inside the developing ovules of host conifers and, until recently, oviposition was believed to occur only in fertilized ovules. Ovule development begins just after pollination, but stops if cells are not fertilized. The morphological stage of cone development at the time of oviposition by seed chalcids has been established for many species; however, knowledge of ovule development at that time has been documented for only one species, M. spermotrophus. Megastigmus spermotrophus oviposits in Douglas-fir ovules after pollination but before fertilization. Unlike the unfertilized ovules, those containing a M. spermotrophus larva continue to develop, whether fertilized or not, stressing the need to broaden our understanding of the insect plant interactions for this entire genus. To achieve this task, we reviewed the scientific literature and assembled information pertaining to the timing of oviposition and to the pollination and fertilization periods of their respective host(s). More specifically, we were searching for circumstantial evidence that other species of Megastigmus associated with conifers could behave (i.e., oviposit before ovule fertilization) and impact on female gametophyte (i.e., prevent abortion) like M. spermotrophus. The evidence from our compilation suggests that seed chalcids infesting Pinaceae may also oviposit before ovule fertilization, just like M. spermotrophus, whereas those infesting Cupressaceae seemingly oviposit after ovule fertilization. Based on this evidence, we hypothesize that all species of Megastigmus

  14. Some conifer clades contribute substantial amounts of leaf waxes to sedimentary archives

    NASA Astrophysics Data System (ADS)

    Diefendorf, A. F.; Wing, S. L.; Leslie, A. B.; Freeman, K. H.

    2014-12-01

    Leaf waxes (i.e. n-alkanes, n-alkanoic acids) and their carbon isotopes (δ13C) are commonly used to track past changes in the carbon cycle or plant ecophysiology. Previous studies indicated that conifer n-alkane concentrations are lower than in angiosperms and that 13C fractionation during n-alkane synthesis (ɛlipid) is smaller than in angiosperms. These prior studies, however, sampled a limited phylogenetic and geographic subset of conifers, leaving out many important subtropical and Southern Hemisphere groups that were once widespread and common components of fossil assemblages. To expand on previous work, we collected 44 conifer species from the University of California Botanical Garden at Berkeley, capturing all extant conifer families and most extant genera. By collecting all specimens at a common site we attempted to minimize the confounding effects of climate, allowing phylogenetic patterns in the δ13C of leaf waxes to be expressed more strongly. We find that Pinaceae, including many North American species used in previous studies, have very low or no n-alkanes. However, other conifer groups have significant concentrations of n-alkanes, especially the Araucariaceae (Norfolk Island pines), Podocarpaceae (common in the Southern Hemisphere), and many species of Cupressaceae (junipers and relatives). Within the Cupressaceae, we find total n-alkane concentrations are high in subfamilies Cupressoideae and Callitroideae, but significantly lower in the early diverging taxodioid lineages (including bald cypress and redwood). Individual n-alkane chain lengths have a weak phylogenetic signal, except for n-C29 alkane, but when combined using average chain length (ACL), a strong phylogenetic signal emerges. The strong phylogenetic signal in ACL reinforces that it is strongly influenced by factors other than climate. An analysis of ɛlipid indicates a strong phylogenetic signal in which the smallest biosynthetic fractionation occurs in Pinaceae and the largest in

  15. Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

    PubMed Central

    Harris, Stephen E.; O’Neill, Rachel J.; Munshi-South, Jason

    2014-01-01

    Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of non-model species. We utilized two Next Generation Sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby, and assembled a reference transcriptome using 1,080,065,954 SOLiD 5500XL (75 bp) reads and 3,052,640 454 GS FLX + reads. The reference contained 40,908 contigs with a N50 = 1,044 bp and a total content of 30.06 Megabases (Mb). Contigs were annotated from comparisons to Mus musculus (39.96% annotated) Uniprot databases. We identified 104,655 high quality single nucleotide polymorphisms (SNPs) and 65 single sequence repeats (SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation. PMID:24980186

  16. The enigma of effective pathlength for 18O enrichment in leaf water of conifers

    NASA Astrophysics Data System (ADS)

    Roden, J. S.; Kahmen, A.; Buchmann, N. C.; Siegwolf, R. T.

    2013-12-01

    The stable isotopes of oxygen (δ18O) in tree ring cellulose provide valuable proxy information about past environments and climate. Mechanistic models have been used to clarify the important drivers of isotope fractionation and help interpret δ18O variation in tree rings. A critical component to these models is an estimate of leaf water enrichment. However, standard models seldom accurately predict 18O enrichment in conifer needles and Péclet corrections often require effective pathlengths (L) that seem unreasonable from the perspective of needle morphology (>0.5 m). To analyze the potential role of path length on the Péclet effect in conifers we carried out experiments in controlled environment chambers. We exposed seedlings of six species of conifer (Abies alba, Larix decidua, Picea abies, Pinus cembra, P. sylvestris, Taxus bacata), that differ in needle morphology, to four different vapor pressure deficits (VPD), in order to modify transpiration rates (E) and leaf water 18O enrichment. Environmental and δ18O data (leaf, stem and chamber water vapor) were collected to parameterize leaf water models. Cross-sections of needles were sampled for an analysis of needle anatomy. Conifer needles have a single strand of vascular tissue making pathlength determinations through anatomical assessments possible. The six species differed in mesophyll distance (measured from endodermis to epidermis) and cell number, with Pinus and Picea species having the shortest distance and Abies and Taxus the longest (flat needle morphology). Other anatomical measures (transfusion distance, cell size etc.) did not differ significantly. A suberized strip was apparent in the endodermis of all species except Taxus and Abies. Conifer needles have a large proportion (from 0.2 to 0.4) of needle cross-sectional area in vascular tissues that may not be subject to evaporative enrichment. As expected, leaf water δ18O and E responded strongly to VPD and standard models (Craig

  17. The Paleocene Eocene carbon isotope excursion in higher plant organic matter: Differential fractionation of angiosperms and conifers in the Arctic

    NASA Astrophysics Data System (ADS)

    Schouten, Stefan; Woltering, Martijn; Rijpstra, W. Irene C.; Sluijs, Appy; Brinkhuis, Henk; Sinninghe Damsté, Jaap S.

    2007-06-01

    A study of upper Paleocene-lower Eocene (P-E) sediments deposited on the Lomonosov Ridge in the central Arctic Ocean reveals relatively high abundances of terrestrial biomarkers. These include dehydroabietane and simonellite derived from conifers (gymnosperms) and a tetra-aromatic triterpenoid derived from angiosperms. The relative percentage of the angiosperm biomarker of the summed angiosperm + conifer biomarkers was increased at the end of the Paleocene-Eocene thermal maximum (PETM), different when observed with pollen counts which showed a relative decrease in angiosperm pollen. Stable carbon isotopic analysis of these biomarkers shows that the negative carbon isotope excursion (CIE) during the PETM amounts to 3‰ for both conifer biomarkers, dehydroabietane and simonellite, comparable to the magnitude of the CIE inferred from marine carbonates, but significantly lower than the 4.5‰ of the terrestrial C 29n-alkane [M. Pagani, N. Pedentchouk, M. Huber, A. Sluijs, S. Schouten, H. Brinkhuis, J.S. Sinninghe Damsté, G.R. Dickens, and the IODP Expedition 302 Expedition Scientists (2006), Arctic's hydrology during global warming at the Paleocene-Eocene thermal maximum. Nature, 442, 671-675.], which is a compound sourced by both conifers and angiosperms. Conspicuously, the angiosperm-sourced aromatic triterpane shows a much larger CIE of 6‰ and suggests that angiosperms increased in their carbon isotopic fractionation during the PETM. Our results thus indicate that the 4.5‰ C 29n-alkane CIE reported previously represents the average CIE of conifers and angiosperms at this site and suggest that the large and variable CIE observed in terrestrial records may be partly explained by the variable contributions of conifers and angiosperms. The differential response in isotopic fractionation of angiosperms and conifers points to different physiological responses of these vegetation types to the rise in temperature, humidity, and greenhouse gases during the PETM.

  18. Anisotropic nanolaminated CoNiFe cores integrated into microinductors for high-frequency dc-dc power conversion

    NASA Astrophysics Data System (ADS)

    Kim, Jooncheol; Kim, Minsoo; Kim, Jung-Kwun; Herrault, Florian; Allen, Mark G.

    2015-11-01

    This paper presents a rectangular, anisotropic nanolaminated CoNiFe core that possesses a magnetically hard axis in the long geometric axis direction. Previously, we have developed nanolaminated cores comprising tens to hundreds of layers of 300-1000 nm thick metallic alloys (i.e. Ni80Fe20 or Co44Ni37Fe19) based on sequential electrodeposition, demonstrating suppressed eddy-current losses at MHz frequencies. In this work, magnetic anisotropy was induced to the nanolaminated CoNiFe cores by applying an external magnetic field (50-100 mT) during CoNiFe film electrodeposition. The fabricated cores comprised tens to hundreds of layers of 500-1000 nm thick CoNiFe laminations that have the hard-axis magnetic property. Packaged in a 22-turn solenoid test inductor, the anisotropic core showed 10% increased effective permeability and 25% reduced core power losses at MHz operation frequency, compared to an isotropic core of the identical geometry. Operating the anisotropic nanolaminated CoNiFe core in a step-down dc-dc converter (15 V input to 5 V output) demonstrated 81% converter efficiency at a switching frequency of 1.1 MHz and output power of 6.5 W. A solenoid microinductor with microfabricated windings integrated with the anisotropic nanolaminated CoNiFe core was fabricated, demonstrating a constant inductance of 600 nH up to 10 MHz and peak quality factor exceeding 20 at 4 MHz. The performance of the microinductor with the anisotropic nanolaminated CoNiFe core is compared with other previously reported microinductors.

  19. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies

    PubMed Central

    2015-01-01

    Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas. PMID:26307380

  20. Headwater riparian invertebrate communities associated with red alder and conifer wood and leaf litter in southeastern Alaska

    USGS Publications Warehouse

    LeSage, C.M.; Merritt, R.W.; Wipfli, M.S.

    2005-01-01

    We examined how management of young upland forests in southeastern Alaska affect riparian invertebrate taxa richness, density, and biomass, in turn, potentially influencing food abundance for fish and wildlife. Southeastern Alaska forests are dominated by coniferous trees including Sitka spruce (Picea sitchensis (Bong.) Carr.), western hemlock (Tsuga heterophylla (Raf.) Sarg.), with mixed stands of red cedar (Thuja plicata Donn.). Red alder (Alnus rubra Bong.) is hypothesized to influence the productivity of young-growth conifer forests and through forest management may provide increased riparian invertebrate abundance. To compare and contrast invertebrate densities between coniferous and alder riparian habitats, leaf litter and wood debris (early and late decay classes) samples were collected along eleven headwater streams on Prince of Wales Island, Alaska, during the summers of 2000 and 2001. Members of Acarina and Collembola were the most abundant taxa collected in leaf litter with alder litter having significantly higher mean taxa richness than conifer litter. Members of Acarina were the most abundant group collected on wood debris and alder wood had significantly higher mean taxa richness and biomass than conifer wood. Alder wood debris in more advanced decay stages had the highest mean taxa richness and biomass, compared to other wood types, while conifer late decay wood debris had the highest densities of invertebrates. The inclusion of alder in young-growth conifer forests can benefit forest ecosystems by enhancing taxa richness and biomass of riparian forest invertebrates. ?? 2005 by the Northwest Scientific Association. All rights reserved.

  1. High-frequency permeability of electroplated CoNiFe and CoNiFe-C alloys

    NASA Astrophysics Data System (ADS)

    Rhen, Fernando M. F.; McCloskey, Paul; O'Donnell, Terence; Roy, Saibal

    We have investigated CoNiFe and CoNiFe-C electrodeposited by pulse reverse plating (PRP) and direct current (DC) techniques. CoNiFe(PRP) films with composition Co 59.4Fe 27.7Ni 12.8 show coercivity of 95 A m -1 (1.2 Oe) and magnetization saturation flux ( μ0Ms) of 1.8 T. Resistivity of CoNiFe (PRP) is about 24 μΩ cm and permeability remains almost constant μr' ˜475 up to 30 MHz with a quality factor ( Q) larger than 10. Additionally, the permeability spectra analysis shows that CoNiFe exhibits a classical eddy current loss at zero bias field and ferromagnetic resonance (FMR) when biased with 0.05 T. Furthermore, a crossover between eddy current and FMR loss is observed for CoNiFe-PRP when baised with 0.05 T. DC and PRP plated CoNiFe-C, which have resistivity and permeability of 85, 38 μΩ cm, μr'=165 and 35 with Q>10 up to 320 MHz, respectively, showed only ferromagnetic resonance losses. The ferromagnetic resonance peaks in CoNiFe and CoNiFe-C are broad and resembles a Gaussian distribution of FMR frequencies. The incorporation of C to CoNiFe reduces eddy current loss, but also reduces the FMR frequency.

  2. Canopy structure of tropical and sub-tropical rain forests in relation to conifer dominance analysed with a portable LIDAR system

    PubMed Central

    Aiba, Shin-ichiro; Akutsu, Kosuke; Onoda, Yusuke

    2013-01-01

    Background and Aims Globally, conifer dominance is restricted to nutient-poor habitats in colder, drier or waterlogged environments, probably due to competition with angiosperms. Analysis of canopy structure is important for understanding the mechanism of plant coexistence in relation to competition for light. Most conifers are shade intolerant, and often have narrow, deep, conical crowns. In this study it is predicted that conifer-admixed forests have less distinct upper canopies and more undulating canopy surfaces than angiosperm-dominated forests. Methods By using a ground-based, portable light detection and ranging (LIDAR) system, canopy structure was quantified for old-growth evergreen rainforests with varying dominance of conifers along altitudinal gradients (200–3100 m a.s.l.) on tropical and sub-tropical mountains (Mount Kinabalu, Malaysian Borneo and Yakushima Island, Japan) that have different conifer floras. Key Results Conifers dominated at higher elevations on both mountains (Podocarpaceae and Araucariaceae on Kinabalu and Cupressaceae and Pinaceae on Yakushima), but conifer dominance also varied with soil/substrate conditions on Kinabalu. Conifer dominance was associated with the existence of large-diameter conifers. Forests with higher conifer dominance showed a canopy height profile (CHP) more skewed towards the understorey on both Kinabalu and Yakushima. In contrast, angiosperm-dominated forests had a CHP skewed towards upper canopy, except for lowland dipterocarp forests and a sub-alpine scrub dominated by small-leaved Leptospermum recurvum (Myrtaceae) on Kinabalu. Forests with a less dense upper canopy had more undulating outer canopy surfaces. Mixed conifer–angiosperm forests on Yakushima and dipterocarp forests on Kinabalu showed similar canopy structures. Conclusions The results generally supported the prediction, suggesting that lower growth of angiosperm trees (except L. recurvum on Kinabalu) in cold and nutrient-poor environments

  3. Ectomycorrhizal Community Structure and Soil Characteristics of Mature Lodgepole Pine (Pinus Contorta) and Adjacent Stands of Old Growth Mixed Conifer in Yellowstone National Park, Wyoming USA

    NASA Technical Reports Server (NTRS)

    Douglas, Robert B.; Parker, V. Thomas; Cullings, Kenneth W.; Sun, Sidney (Technical Monitor)

    2003-01-01

    Forest development patterns following disturbance are known to influence the physical and chemical attributes of soils at different points in time. Changes in soil resources are thought to have a corresponding effect on ectomycorrhizal (ECM) community structure. We used molecular methods to compare below-ground ECM species richness, composition, and abundance between adjacent stands of homogenous lodgepole pine and old growth mixed conifer in Yellowstone National Park (YNP). In each stand-type we collected soil cores to both identify mycorrhizae and assess soil chemistry. Although no statistical difference was observed in the mean number of ECM root tips per core between stand types, the total number of species identified (85 versus 35) and the mean number of species per core (8.8 +/- 0.6 versus 2.5 +/- 0.3) were significantly higher in lodgepole pine. Differences between the actual and estimated species richness levels indicated that these forest types support a high number of ECM species and that undersampling was severe. Species compositions were widely disparate between stands where only four species were shared out of a total of 116. Soil analysis also revealed that mixed conifer was significantly lower in pH, but higher in organic matter, potassium, phosphorus, and ammonium when compared to lodgepole pine stands. Species richness per core was correlated with these chemical data, however, analysis of covariance indicated that stand type was the only statistically significant factor in the observed difference in species richness. Our data suggest that ECM fungal richness increases as homogenous lodgepole pine stands grow and mature, but declines after Engelmann spruce and subalpine fir colonize. Despite difficulties linking species composition with soil chemistry, there are a variety of physical and chemical factors that could be influencing ECM community structure. Future field experiments are necessary to test some of the mechanisms potentially operating

  4. Fire regimes, forest change, and self-organization in an old-growth mixed-conifer forest, Yosemite National Park, USA.

    PubMed

    Scholl, Andrew E; Taylor, Alan H

    2010-03-01

    Fire is recognized as a keystone process in dry mixed-conifer forests that have been altered by decades of fire suppression, Restoration of fire disturbance to these forests is a guiding principle of resource management in the U.S. National Park Service. Policy implementation is often hindered by a poor understanding of forest conditions before fire exclusion, the characteristics of forest changes since excluding fire, and the influence of topographic or self-organizing controls on forest structure. In this study the spatial and temporal characteristics of fire regimes and forest structure are reconstructed in a 2125-ha mixed-conifer forest. Forests were multi-aged, burned frequently at low severity and fire-return interval, and forest structure did not vary with slope aspect, elevation, or slope position. Fire exclusion has caused an increase in forest density and basal area and a compositional shift to shade-tolerant and fire-intolerant species. The median point fire-return interval and extent of a fire was 10 yr and 115 ha, respectively. The pre-Euro-American settlement fire rotation of 13 yr increased to 378 yr after 1905. The position of fire scars within tree rings indicates that 79% of fires burned in the midsummer to fall period. The spatial pattern of burns exhibited self-organizing behavior. Area burned was 10-fold greater when an area had not been burned by the previous fire. Fires were frequent and widespread, but patches of similar aged trees were < 0.2 ha, suggesting small fire-caused canopy openings. Managers need to apply multiple burns at short intervals for a sustained period to reduce surface fuels and create small canopy openings characteristic of the reference forest. By coupling explicit reference conditions with consideration of current conditions and projected climate change, management activities can balance restoration and risk management.

  5. Mapping and monitoring conifer mortality using remote sensing in the Lake Tahoe Basin

    SciTech Connect

    Macomber, S.A.; Woodcock, C.E. )

    1994-12-01

    A prolonged drought in the western US has resulted in alarming levels of mortality in conifer forests. Satellite remote sensing holds the potential for mapping and monitoring the effects of such environmental changes over large geographic areas in a timely manner. Results from the application of a forest canopy reflectance model using multitemporal Landsat TM imagery and field measurements, indicate conifer mortality can be effectively mapped and inventoried. The test area for this project is the Lake Tahoe Basin Management Unit in the Sierra Nevada of California. The Landsat TM images are from the summers of 1988 and 1991. The Li-Strahler canopy model estimates several forest stand parameters, including tree size and canopy cover for each conifer stand, from reflectance values in satellite imagery. The difference in cover estimates between the dates forms the basis for stratifying stands into mortality classes, which are used as both themes in a map and the basis of the field sampling design. Field measurements from 61 stands collected in the summer of 1992 indicate 15% of the original timber volume in the true fir zone died between 1988 and 1992. The resulting low standard error of 11% for this estimate indicates the utility of these mortality classes for detecting areas of high mortality. Also, the patterns in the estimated mean timber volume loss for each class follow the expected trends. The results of this project are immediately useful for fire hazard management, by providing both estimates of the degree of overall mortality and maps showing its location. They also indicate current remote sensing technology may be useful for monitoring the changes in vegetation that are expected to result from climate change.

  6. Conifer density within lake catchments predicts fish mercury concentrations in remote subalpine lakes.

    PubMed

    Eagles-Smith, Collin A; Herring, Garth; Johnson, Branden; Graw, Rick

    2016-05-01

    Remote high-elevation lakes represent unique environments for evaluating the bioaccumulation of atmospherically deposited mercury through freshwater food webs, as well as for evaluating the relative importance of mercury loading versus landscape influences on mercury bioaccumulation. The increase in mercury deposition to these systems over the past century, coupled with their limited exposure to direct anthropogenic disturbance make them useful indicators for estimating how changes in mercury emissions may propagate to changes in Hg bioaccumulation and ecological risk. We evaluated mercury concentrations in resident fish from 28 high-elevation, sub-alpine lakes in the Pacific Northwest region of the United States. Fish total mercury (THg) concentrations ranged from 4 to 438 ng/g wet weight, with a geometric mean concentration (±standard error) of 43 ± 2 ng/g ww. Fish THg concentrations were negatively correlated with relative condition factor, indicating that faster growing fish that are in better condition have lower THg concentrations. Across the 28 study lakes, mean THg concentrations of resident salmonid fishes varied as much as 18-fold among lakes. We used a hierarchal statistical approach to evaluate the relative importance of physiological, limnological, and catchment drivers of fish Hg concentrations. Our top statistical model explained 87% of the variability in fish THg concentrations among lakes with four key landscape and limnological variables: catchment conifer density (basal area of conifers within a lake's catchment), lake surface area, aqueous dissolved sulfate, and dissolved organic carbon. Conifer density within a lake's catchment was the most important variable explaining fish THg concentrations across lakes, with THg concentrations differing by more than 400 percent across the forest density spectrum. These results illustrate the importance of landscape characteristics in controlling mercury bioaccumulation in fish.

  7. Conifer density within lake catchments predicts fish mercury concentrations in remote subalpine lakes

    USGS Publications Warehouse

    Eagles-Smith, Collin A.; Herring, Garth; Johnson, Branden L.; Graw, Rick

    2016-01-01

    Remote high-elevation lakes represent unique environments for evaluating the bioaccumulation of atmospherically deposited mercury through freshwater food webs, as well as for evaluating the relative importance of mercury loading versus landscape influences on mercury bioaccumulation. The increase in mercury deposition to these systems over the past century, coupled with their limited exposure to direct anthropogenic disturbance make them useful indicators for estimating how changes in mercury emissions may propagate to changes in Hg bioaccumulation and ecological risk. We evaluated mercury concentrations in resident fish from 28 high-elevation, sub-alpine lakes in the Pacific Northwest region of the United States. Fish total mercury (THg) concentrations ranged from 4 to 438 ng/g wet weight, with a geometric mean concentration (±standard error) of 43 ± 2 ng/g ww. Fish THg concentrations were negatively correlated with relative condition factor, indicating that faster growing fish that are in better condition have lower THg concentrations. Across the 28 study lakes, mean THg concentrations of resident salmonid fishes varied as much as 18-fold among lakes. We used a hierarchal statistical approach to evaluate the relative importance of physiological, limnological, and catchment drivers of fish Hg concentrations. Our top statistical model explained 87% of the variability in fish THg concentrations among lakes with four key landscape and limnological variables: catchment conifer density (basal area of conifers within a lake's catchment), lake surface area, aqueous dissolved sulfate, and dissolved organic carbon. Conifer density within a lake's catchment was the most important variable explaining fish THg concentrations across lakes, with THg concentrations differing by more than 400 percent across the forest density spectrum. These results illustrate the importance of landscape characteristics in controlling mercury bioaccumulation in fish.

  8. Conifer density within lake catchments predicts fish mercury concentrations in remote subalpine lakes.

    PubMed

    Eagles-Smith, Collin A; Herring, Garth; Johnson, Branden; Graw, Rick

    2016-05-01

    Remote high-elevation lakes represent unique environments for evaluating the bioaccumulation of atmospherically deposited mercury through freshwater food webs, as well as for evaluating the relative importance of mercury loading versus landscape influences on mercury bioaccumulation. The increase in mercury deposition to these systems over the past century, coupled with their limited exposure to direct anthropogenic disturbance make them useful indicators for estimating how changes in mercury emissions may propagate to changes in Hg bioaccumulation and ecological risk. We evaluated mercury concentrations in resident fish from 28 high-elevation, sub-alpine lakes in the Pacific Northwest region of the United States. Fish total mercury (THg) concentrations ranged from 4 to 438 ng/g wet weight, with a geometric mean concentration (±standard error) of 43 ± 2 ng/g ww. Fish THg concentrations were negatively correlated with relative condition factor, indicating that faster growing fish that are in better condition have lower THg concentrations. Across the 28 study lakes, mean THg concentrations of resident salmonid fishes varied as much as 18-fold among lakes. We used a hierarchal statistical approach to evaluate the relative importance of physiological, limnological, and catchment drivers of fish Hg concentrations. Our top statistical model explained 87% of the variability in fish THg concentrations among lakes with four key landscape and limnological variables: catchment conifer density (basal area of conifers within a lake's catchment), lake surface area, aqueous dissolved sulfate, and dissolved organic carbon. Conifer density within a lake's catchment was the most important variable explaining fish THg concentrations across lakes, with THg concentrations differing by more than 400 percent across the forest density spectrum. These results illustrate the importance of landscape characteristics in controlling mercury bioaccumulation in fish. PMID:26854697

  9. Nitric acid dry deposition to conifer forests: Niwot Ridge spruce-fir-pine study

    USGS Publications Warehouse

    Sievering, H.; Kelly, T.; McConville, G.; Seibold, C.; Turnipseed, A.

    2001-01-01

    The dry deposition velocity of nitric acid, Vd(HNO3), over a 12-m (mean height) spruce-fir forest at Niwot Ridge, Colorado was estimated during 13 daytime periods using the flux-gradient approach. Turbulence intensity at this site is high (mean u* of 0.65ms-1 with u of 2.9ms-1) and contributed to the large observed Vd(HNO3). The overriding contributor is identified to be the small aerodynamic needle width of the conifer trees. Two cases had inflated Vd(HNO3) due to height-differentiated nitric acid loss to soil-derived particle surfaces. Not considering these cases, the mean Vd(HNO3) was 7.6cms-1. The mean laminar boundary layer resistance (Rb) was found to be 7.8sm-1 (of similar magnitude to that of the aerodynamic resistance, 8.5sm-1). The data-determined Rb is bracketed by two theoretical estimates of the mean Rb, 5.9 and 8.6sm-1, that include consideration of the small canopy length scale (aerodynamic needle width), 1mm or less, at this conifer forest. However, the poor correlation of data-determined Rb values with both sets of theoretical estimates indicates that measurement error needs to be reduced and/or improved formulations of theoretical Rb values are in order. The large observed Vd(HNO3) at this conifer forest site is attributed to high turbulence intensity, and, especially, to small aerodynamic needle width. Copyright ?? 2001 Elsevier Science Ltd.

  10. Quantifying thermal constraints on carbon and water fluxes in a mixed-conifer sky island ecosystem

    NASA Astrophysics Data System (ADS)

    Braun, Z.; Minor, R. L.; Potts, D. L.; Barron-Gafford, G. A.

    2012-12-01

    Western North American forests represent a potential, yet uncertain, sink for atmospheric carbon. Revealing how predicted climatic conditions of warmer temperatures and longer inter-storm periods of moisture stress might influence the carbon status of these forests requires a fuller understanding of plant functional responses to abiotic stress. While data related to snow dominated montane ecosystems has become more readily available to parameterize ecosystem function models, there is a paucity of data available for Madrean sky island mixed-conifer forests, which receive about one third of their precipitation from the North American Monsoon. Thus, we quantified ecophysiological responses to moisture and temperature stress in a Madrean mixed-conifer forest near Tucson, Arizona, within the footprint of the Mt. Bigelow Eddy Covariance Tower. In measuring a series of key parameters indicative of carbon and water fluxes within the dominant species across pre-monsoon and monsoon conditions, we were able to develop a broader understanding of what abiotic drivers are most restrictive to plant performance in this ecosystem. Within Pinus ponderosa (Ponderosa Pine), Pseudotsuga menziesii (Douglas Fir), and Pinus strobiformis (Southwestern White Pine) we quantified: (i) the optimal temperature (Topt) for maximum photosynthesis (Amax), (ii) the range of temperatures over which photosynthesis was at least 50% of Amax (Ω50), and (iii) each conifer's water use efficiency (WUE) to relate to the balance between carbon uptake and water loss in this high elevation semiarid ecosystem. Our findings support the prediction that photosynthesis decreases under high temperatures (>30°C) among the three species we measured, regardless of soil moisture status. However, monsoon moisture reduced sensitivity to temperature extremes and fluctuations (Ω50), which substantially magnified total photosynthetic productivity. In particular, wet conditions enhanced Amax the most dramatically for P

  11. Development of nuclear and chloroplast microsatellite markers for the endangered conifer Callitris sulcata (Cupressaceae)1

    PubMed Central

    Sakaguchi, Shota; Lannuzel, Guillaume; Fogliani, Bruno; Wulff, Adrien S.; L’Huillier, Laurent; Kurata, Seikan; Ueno, Saneyoshi; Isagi, Yuji; Tsumura, Yoshihiko; Ito, Motomi

    2015-01-01

    Premise of the study: Microsatellite markers were developed for Callitris sulcata (Cupressaceae), an endangered conifer species in New Caledonia. Methods and Results: Using sequencing by synthesis (SBS) of an RNA-Seq library, 15 polymorphic nuclear and chloroplast microsatellite markers were developed. When evaluated with 48 individuals, these markers showed genetic variations ranging from two to 15 alleles and expected heterozygosity ranging from 0 to 0.881. Conclusions: These markers will be useful for examining the genetic diversity and structure of remaining wild populations and improving the genetic status of ex situ populations. PMID:26312198

  12. Measuring near infrared spectral reflectance changes from water stressed conifer stands with AIS-2

    NASA Technical Reports Server (NTRS)

    Riggs, George; Running, Steven W.

    1987-01-01

    Airborne Imaging Spectrometer-2 (AIS-2) data was acquired over two paired conifer stands for the purpose of detecting differences in spectral reflectance between stressed and natural canopies. Water stress was induced in a stand of Norway spruce and white pine by severing the sapwood near the ground. Water stress during the AIS flights was evaluated through shoot water potential and relative water content measurements. Preliminary analysis with raw AIS-2 data using SPAM indicates that there were small, inconsistent differences in absolute spectral reflectance in the near infrared 0.97 to 1.3 micron between the stressed and natural canopies.

  13. Molecular Characterization of Fusarium oxysporum and Fusarium commune Isolates from a Conifer Nursery.

    PubMed

    Stewart, Jane E; Kim, Mee-Sook; James, Robert L; Dumroese, R Kasten; Klopfenstein, Ned B

    2006-10-01

    ABSTRACT Fusarium species can cause severe root disease and damping-off in conifer nurseries. Fusarium inoculum is commonly found in most container and bareroot nurseries on healthy and diseased seedlings, in nursery soils, and on conifer seeds. Isolates of Fusarium spp. can differ in virulence; however, virulence and colony morphology are not correlated. Forty-one isolates of Fusarium spp., morphologically indistinguishable from F. oxysporum, were collected from nursery samples (soils, healthy seedlings, and diseased seedlings). These isolates were characterized by amplified fragment length polymorphism (AFLP) and DNA sequencing of nuclear rDNA (internal transcribed spacer including 5.8S rDNA), mitochon-drial rDNA (small subunit [mtSSU]), and nuclear translation elongation factor 1-alpha. Each isolate had a unique AFLP phenotype. Out of 121 loci, 111 (92%) were polymorphic; 30 alleles were unique to only highly virulent isolates and 33 alleles were unique to only isolates nonpathogenic on conifers. Maximum parsimony and Bayesian analyses of DNA sequences from all three regions and the combined data set showed that all highly virulent isolates clearly separated into a common clade that contained F. commune, which was recently distinguished from its sister taxon, F. oxysporum. Interestingly, all but one of the nonpathogenic isolates grouped into a common clade and were genetically similar to F. oxysporum. The AFLP cladograms had similar topologies when compared with the DNA-based phylograms. Although all tested isolates were morphologically indistinguishable from F. oxysporum based on currently available monographs, some morphological traits can be plastic and unreliable for identification of Fusarium spp. We consider the highly virulent isolates to be F. commune based on strong genetic evidence. To our knowledge, this is the first reported evidence that shows F. commune is a cause of Fusarium disease (root rot and dampingoff) on Douglas-fir seedlings. Furthermore

  14. Fuel models to predict fire behavior in untreated conifer slash. Forest Service research note (final)

    SciTech Connect

    Salazar, L.A.; Bevins, C.D.

    1984-11-01

    Fire behavior in untreated slash of nine conifer species was simulated for 10 successive years after logging. Two aging factors that affect fire behavior--fuel bed compaction and foliage retention--were modeled by least squares regression techniques. On the basis of spread rate and flame length for a set of weather observations, standard Northern Forest Fire Laboratory fuel models were chosen to predict fire behavior for aging slash of each species at three initial fuel loadings. Differences in the standard fuel model sequences best representing aging process among species were most influenced by foliage surface-area-to-volume ratio, and such differences increased as initial fuel load increased.

  15. Lentil genetic and genomic resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lentil (Lens culinaris spp. culinaris) has a long history associated with the early civilizations 11,000 BP in southwestern Asia. The progenitor taxon is Lens culinaris spp. orientalis. The primary source of germplasm for lentil crop improvement is from the International Center for Agricultural Rese...

  16. Temperature effects on nitrogen form uptake by seedling roots of three contrasting conifers.

    PubMed

    Boczulak, S A; Hawkins, B J; Roy, R

    2014-05-01

    Plant species may show a preference for uptake of particular nitrogen (N) forms, but little is known about how N form preference is influenced by soil temperature. Potential future changes in soil N form availability and plant N form preference in warmer soils might shift competitive interactions among forest tree species. We compared the N uptake and growth of three conifer species from contrasting environments grown at rhizosphere temperatures of 10, 16 or 20 °C and supplied with ammonium (NH4 (+)) or nitrate (NO3 (-)) or a mix of arginine and alanine. Short-term N uptake was assessed using ion-selective microelectrodes and application of (15)N, and long-term uptake was assessed by plant N status. Species exhibited preferences for particular N forms, and these preferences related to the N form most available in native soils. Specifically, Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) showed a preference for nitrate (a N form commonly found in warmer areas), Sitka spruce (Picea sitchensis (Bong.) Carr.) preferred ammonium (a N form abundant in cold soils) and Engelmann spruce (Picea engelmannii Parry ex Engelm.) showed a preference for ammonium and organic N (organic N is often abundant in cold soils). Relative N form preference, as indicated by plant growth, changed with temperature in some species, indicating that these species could acclimate to changing rhizosphere temperatures. Understanding how conifers utilize available soil nutrients at different temperatures can help to predict species' future performance as soil temperatures rise. PMID:24831958

  17. Specialised emission pattern of leaf trace in a late Permian (253 million-years old) conifer

    PubMed Central

    Wei, Hai-Bo; Feng, Zhuo; Yang, Ji-Yuan; Chen, Yu-Xuan; Shen, Jia-Jia; He, Xiao-Yuan

    2015-01-01

    Leaf traces are important structures in higher plants that connect leaves and the stem vascular system. The anatomy and emission pattern of leaf traces are well studied in extant vascular plants, but remain poorly understood in fossil lineages. We quantitatively analysed the leaf traces in the late Permian conifer Ningxiaites specialis from Northwest China based on serial sections through pith, primary and secondary xylems. A complete leaf traces emission pattern of a conifer is presented for the first time from the late Palaeozoic. Three to five monarch leaf traces are grouped in clusters, arranged in a helical phyllotaxis. The leaf traces in each cluster can be divided into upper, middle and lower portions, and initiate at the pith periphery and cross the wood horizontally. The upper leaf trace increases its diameter during the first growth increment and then diminishes completely, which indicates leaf abscission at the end of the first year. The middle trace immediately bifurcates once or twice to form two or three vascular bundles. The lower trace persists as a single bundle during its entire length. The intricate leaf trace dynamics indicates this fossil plant had a novel evolutionary habit by promoting photosynthetic capability for the matured plant. PMID:26198410

  18. Conifer species adapt to low-rainfall climates by following one of two divergent pathways.

    PubMed

    Brodribb, Timothy J; McAdam, Scott A M; Jordan, Gregory J; Martins, Samuel C V

    2014-10-01

    Water stress is one of the primary selective forces in plant evolution. There are characters often cited as adaptations to water stress, but links between the function of these traits and adaptation to drying climates are tenuous. Here we combine distributional, climatic, and physiological evidence from 42 species of conifers to show that the evolution of drought resistance follows two distinct pathways, both involving the coordinated evolution of tissues regulating water supply (xylem) and water loss (stomatal pores) in leaves. Only species with very efficient stomatal closure, and hence low minimum rates of water loss, inhabit dry habitats, but species diverged in their apparent mechanism for maintaining closed stomata during drought. An ancestral mechanism found in Pinaceae and Araucariaceae species relies on high levels of the hormone abscisic acid (ABA) to close stomata during water stress. A second mechanism, found in the majority of Cupressaceae species, uses leaf desiccation rather than high ABA levels to close stomata during sustained water stress. Species in the latter group were characterized by xylem tissues with extreme resistance to embolism but low levels of foliar ABA after 30 d without water. The combination of low levels of ABA under stress with cavitation-resistant xylem enables these species to prolong stomatal opening during drought, potentially extending their photosynthetic activity between rainfall events. Our data demonstrate a surprising simplicity in the way conifers evolved to cope with water shortage, indicating a critical interaction between xylem and stomatal tissues during the process of evolution to dry climates. PMID:25246559

  19. Long-term effects of fire severity on oak-conifer dynamics in the southern Cascades.

    PubMed

    Cocking, Matthew I; Varner, J Morgan; Knapp, Eric E

    2014-01-01

    We studied vegetation composition and structure in a mixed conifer-oak ecosystem across a range of fire severity 10 years following wildfire. Sample plots centered on focal California black oaks (Quercus kelloggii) were established to evaluate oak and neighboring tree and shrub recovery across a gradient of fire severity in the southern Cascade Range, USA. Shrub and oak resprouting was strongest around focal oaks where conifer mortality was greatest. Linear modeling revealed negative relationships between California black oak sprout height or basal area and residual overstory tree survival, primarily white fir (Abies concolor). The two dominant competing species, California black oak and white fir, showed opposite responses to fire severity. Sprouting California black oak and associated shrubs dominated in severely burned areas, while surviving, non-sprouting white fir maintained dominance by its height advantage and shading effects in areas that burned with low fire severity. Our results indicate that high-severity fire promotes persistence and restoration of ecosystems containing resprouting species, such as California black oak, that are increasingly rare due to widespread fire exclusion in landscapes that historically experienced more frequent fire. We present a conceptual model based on our results and supported by a synthesis of postfire resprouting dynamics literature. Our results and conceptual model help illuminate long-term postfire vegetation responses and the potential ability of fire to catalyze formation of alternate vegetation community structures that may not be apparent in studies that evaluate postfire effects at shorter time-since-fire intervals or at coarser scales.

  20. Spectral changes in conifers subjected to air pollution and water stress: Experimental studies

    NASA Technical Reports Server (NTRS)

    Westman, Walter E.; Price, Curtis V.

    1988-01-01

    The roles of leaf anatomy, moisture and pigment content, and number of leaf layers on spectral reflectance in healthy, pollution-stressed, and water-stressed conifer needles were examined experimentally. Jeffrey pine (Pinus jeffreyi) and giant sequoia (Sequoiadendron gigantea) were exposed to ozone and acid mist treatments in fumigation chambers; red pine (Pinus resinosa) needles were artificially dried. Infrared reflectance from stacked needles rose with free water loss. In an air-drying experiment, cell volume reductions induced by loss of turgor caused near-infrared reflectance (TM band 4) to drop after most free water was lost. Under acid mist fumigation, stunting of tissue development similarly reduced band 4 reflectance. Both artificial drying and pollutant fumigation caused a blue shift of the red edge of spectral reflectance curves in conifers, attributable to chlorophyll denaturation. Thematic mapper band ratio 4/3 fell and 5/4 rose with increasing pollution stress on artificial drying. Loss of water by air-drying, freeze-drying, or oven-drying enhanced spectral features, due in part to greater scattering and reduced water absorption. Grinding of the leaf tissue further enhanced the spectral features by increasing reflecting surfaces and path length. In a leaf-stacking experiment, an asymptote in visible and infrared reflectance was reached at 7-8 needle layers of red pine.

  1. Conifer species adapt to low-rainfall climates by following one of two divergent pathways

    PubMed Central

    Brodribb, Timothy J.; McAdam, Scott A.M.; Jordan, Gregory J.; Martins, Samuel C.V.

    2014-01-01

    Water stress is one of the primary selective forces in plant evolution. There are characters often cited as adaptations to water stress, but links between the function of these traits and adaptation to drying climates are tenuous. Here we combine distributional, climatic, and physiological evidence from 42 species of conifers to show that the evolution of drought resistance follows two distinct pathways, both involving the coordinated evolution of tissues regulating water supply (xylem) and water loss (stomatal pores) in leaves. Only species with very efficient stomatal closure, and hence low minimum rates of water loss, inhabit dry habitats, but species diverged in their apparent mechanism for maintaining closed stomata during drought. An ancestral mechanism found in Pinaceae and Araucariaceae species relies on high levels of the hormone abscisic acid (ABA) to close stomata during water stress. A second mechanism, found in the majority of Cupressaceae species, uses leaf desiccation rather than high ABA levels to close stomata during sustained water stress. Species in the latter group were characterized by xylem tissues with extreme resistance to embolism but low levels of foliar ABA after 30 d without water. The combination of low levels of ABA under stress with cavitation-resistant xylem enables these species to prolong stomatal opening during drought, potentially extending their photosynthetic activity between rainfall events. Our data demonstrate a surprising simplicity in the way conifers evolved to cope with water shortage, indicating a critical interaction between xylem and stomatal tissues during the process of evolution to dry climates. PMID:25246559

  2. A multiproxy environmental investigation of Holocene wood from a submerged conifer forest in Lake Huron, USA

    NASA Astrophysics Data System (ADS)

    Hunter, R. Douglas; Panyushkina, Irina P.; Leavitt, Steven W.; Wiedenhoeft, Alex C.; Zawiskie, John

    2006-07-01

    Remains of a Holocene drowned forest in southern Lake Huron discovered in 12.5 m of water (164 m above sea level), 4.5 km east of Lexington, Michigan USA (Sanilac site), provided wood to investigate environment and lake history using several proxies. Macrofossil evidence indicates a forest comprised primarily of conifers equivalent to the modern "rich conifer swamp" community, despite generally low regional abundance of these species in pollen records. Ages range from 7095 ± 50 to 6420 ± 70 14C yr BP, but the clustering of stump dates and the development of 2 floating tree-ring chronologies suggest a briefer forest interval of no more than c. 400 years. Dendrochronological analysis indicates an environment with high inter-annual climate variability. Stable-carbon isotope composition falls within the range of modern trees from this region, but the stable-oxygen composition is consistent with warmer conditions than today. Both our tree-ring and isotope data provide support for a warmer environment in this region, consistent with a mid-Holocene thermal maximum. This drowned forest also provides a dated elevation in the Nipissing transgression at about 6420 14C yr BP (7350 cal yr BP) in the southern Lake Huron basin, a few hundred years before reopening of the St. Clair River drainage.

  3. Foliage influences forced convection heat transfer in conifer branches and buds.

    PubMed

    Michaletz, S T; Johnson, E A

    2006-01-01

    Conifer foliage structures affect branch and bud temperature by altering the development and convective resistance of the thermal boundary layer. This paper examines foliage effects on forced convection in branches and buds of Picea glauca (Moench) Voss and Pinus contorta Dougl. Ex. Loud., two species that represent the range of variation in foliage structure among conifers. Forced convection is characterized by a power law relating Nusselt (heat transfer) and Reynolds (boundary layer development) numbers. Data were collected in a laminar flow wind tunnel for free stream velocities of 0.16-6.95 m s(-1). Scaling parameters were compared against literature values for silver cast branch replicas, a bed of real foliage, cylinders, and tube banks. Foliage structures reduced Nusselt numbers (heat transfer) relative to cylinders, which are typically used to approximate leafless branches and buds. Significantly different scaling relationships were observed for all foliage structures considered. Forced convection scaling relationships varied with foliage structure. The scaling relationships reported here account for variation within populations of branches and buds and can be used to characterize forced convection in a forest canopy.

  4. Conifer species adapt to low-rainfall climates by following one of two divergent pathways.

    PubMed

    Brodribb, Timothy J; McAdam, Scott A M; Jordan, Gregory J; Martins, Samuel C V

    2014-10-01

    Water stress is one of the primary selective forces in plant evolution. There are characters often cited as adaptations to water stress, but links between the function of these traits and adaptation to drying climates are tenuous. Here we combine distributional, climatic, and physiological evidence from 42 species of conifers to show that the evolution of drought resistance follows two distinct pathways, both involving the coordinated evolution of tissues regulating water supply (xylem) and water loss (stomatal pores) in leaves. Only species with very efficient stomatal closure, and hence low minimum rates of water loss, inhabit dry habitats, but species diverged in their apparent mechanism for maintaining closed stomata during drought. An ancestral mechanism found in Pinaceae and Araucariaceae species relies on high levels of the hormone abscisic acid (ABA) to close stomata during water stress. A second mechanism, found in the majority of Cupressaceae species, uses leaf desiccation rather than high ABA levels to close stomata during sustained water stress. Species in the latter group were characterized by xylem tissues with extreme resistance to embolism but low levels of foliar ABA after 30 d without water. The combination of low levels of ABA under stress with cavitation-resistant xylem enables these species to prolong stomatal opening during drought, potentially extending their photosynthetic activity between rainfall events. Our data demonstrate a surprising simplicity in the way conifers evolved to cope with water shortage, indicating a critical interaction between xylem and stomatal tissues during the process of evolution to dry climates.

  5. Analysis of freeze-thaw embolism in conifers. The interaction between cavitation pressure and tracheid size.

    PubMed

    Pittermann, Jarmila; Sperry, John S

    2006-01-01

    Ice formation in the xylem sap produces air bubbles that under negative xylem pressures may expand and cause embolism in the xylem conduits. We used the centrifuge method to evaluate the relationship between freeze-thaw embolism and conduit diameter across a range of xylem pressures (Px) in the conifers Pinus contorta and Juniperus scopulorum. Vulnerability curves showing loss of conductivity (embolism) with Px down to -8 MPa were generated with versus without superimposing a freeze-thaw treatment. In both species, the freeze-thaw plus water-stress treatment caused more embolism than water stress alone. We estimated the critical conduit diameter (Df) above which a tracheid will embolize due to freezing and thawing and found that it decreased from 35 microm at a Px of -0.5 MPa to 6 microm at -8 MPa. Further analysis showed that the proportionality between diameter of the air bubble nucleating the cavitation and the diameter of the conduit (kL) declined with increasingly negative Px. This suggests that the bubbles causing cavitation are smaller in proportion to tracheid diameter in narrow tracheids than in wider ones. A possible reason for this is that the rate of dissolving increases with bubble pressure, which is inversely proportional to bubble diameter (La Place's law). Hence, smaller bubbles shrink faster than bigger ones. Last, we used the empirical relationship between Px and Df to model the freeze-thaw response in conifer species.

  6. Control of resin production in Araucaria angustifolia, an ancient South American conifer.

    PubMed

    Perotti, J C; da Silva Rodrigues-Corrêa, K C; Fett-Neto, A G

    2015-07-01

    Araucaria angustifolia is an ancient slow-growing conifer that characterises parts of the Southern Atlantic Forest biome, currently listed as a critically endangered species. The species also produces bark resin, although the factors controlling its resinosis are largely unknown. To better understand this defence-related process, we examined the resin exudation response of A. angustifolia upon treatment with well-known chemical stimulators used in fast-growing conifers producing both bark and wood resin, such as Pinus elliottii. The initial hypothesis was that A. angustifolia would display significant differences in the regulation of resinosis. The effect of Ethrel(®) (ET - ethylene precursor), salicylic acid (SA), jasmonic acid (JA), sulphuric acid (SuA) and sodium nitroprusside (SNP - nitric oxide donor) on resin yield and composition in young plants of A. angustifolia was examined. In at least one of the concentrations tested, and frequently in more than one, an aqueous glycerol solution applied on fresh wound sites of the stem with one or more of the adjuvants examined promoted an increase in resin yield, as well as monoterpene concentration (α-pinene, β-pinene, camphene and limonene). Higher yields and longer exudation periods were observed with JA and ET, another feature shared with Pinus resinosis. The results suggest that resinosis control is similar in Araucaria and Pinus. In addition, A. angustifolia resin may be a relevant source of valuable terpene chemicals, whose production may be increased by using stimulating pastes containing the identified adjuvants.

  7. Stable Water Use Efficiency under Climate Change of Three Sympatric Conifer Species at the Alpine Treeline

    PubMed Central

    Wieser, Gerhard; Oberhuber, Walter; Gruber, Andreas; Leo, Marco; Matyssek, Rainer; Grams, Thorsten Erhard Edgar

    2016-01-01

    The ability of treeline associated conifers in the Central Alps to cope with recent climate warming and increasing CO2 concentration is still poorly understood. We determined tree ring stable carbon and oxygen isotope ratios of Pinus cembra, Picea abies, and Larix decidua trees from 1975 to 2010. Stable isotope ratios were compared with leaf level gas exchange measurements carried out in situ between 1979 and 2007. Results indicate that tree ring derived intrinsic water-use efficiency (iWUE) of P. cembra, P. abies and L. decidua remained constant during the last 36 years despite climate warming and rising atmospheric CO2. Temporal patterns in Δ13C and Δ18O mirrored leaf level gas exchange assessments, suggesting parallel increases of CO2-fixation and stomatal conductance of treeline conifer species. As at the study site soil water availability was not a limiting factor iWUE remained largely stable throughout the study period. The stability in iWUE was accompanied by an increase in basal area increment (BAI) suggesting that treeline trees benefit from both recent climate warming and CO2 fertilization. Finally, our results suggest that iWUE may not change species composition at treeline in the Austrian Alps due to similar ecophysiological responses to climatic changes of the three sympatric study species. PMID:27375653

  8. Stable Water Use Efficiency under Climate Change of Three Sympatric Conifer Species at the Alpine Treeline.

    PubMed

    Wieser, Gerhard; Oberhuber, Walter; Gruber, Andreas; Leo, Marco; Matyssek, Rainer; Grams, Thorsten Erhard Edgar

    2016-01-01

    The ability of treeline associated conifers in the Central Alps to cope with recent climate warming and increasing CO2 concentration is still poorly understood. We determined tree ring stable carbon and oxygen isotope ratios of Pinus cembra, Picea abies, and Larix decidua trees from 1975 to 2010. Stable isotope ratios were compared with leaf level gas exchange measurements carried out in situ between 1979 and 2007. Results indicate that tree ring derived intrinsic water-use efficiency (iWUE) of P. cembra, P. abies and L. decidua remained constant during the last 36 years despite climate warming and rising atmospheric CO2. Temporal patterns in Δ(13)C and Δ(18)O mirrored leaf level gas exchange assessments, suggesting parallel increases of CO2-fixation and stomatal conductance of treeline conifer species. As at the study site soil water availability was not a limiting factor iWUE remained largely stable throughout the study period. The stability in iWUE was accompanied by an increase in basal area increment (BAI) suggesting that treeline trees benefit from both recent climate warming and CO2 fertilization. Finally, our results suggest that iWUE may not change species composition at treeline in the Austrian Alps due to similar ecophysio