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Sample records for monitoring genomic sequences

  1. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  2. Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

    PubMed Central

    2011-01-01

    Background The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. Results A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. Conclusions The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress. PMID:21569398

  3. Multiplexed Fragaria Chloroplast Genome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method to sequence multiple chloroplast genomes that uses the sequencing depth of ultra high throughput sequencing technologies was recently described. Sequencing complete chloroplast genomes can resolve phylogenetic relationships at low taxonomic levels and identify point mutations and indels tha...

  4. SINGLE CELL GENOME SEQUENCING

    PubMed Central

    Yilmaz, Suzan; Singh, Anup K.

    2011-01-01

    Whole genome amplification and next-generation sequencing of single cells has become a powerful approach for studying uncultivated microorganisms that represent 90–99 % of all environmental microbes. Single cell sequencing enables not only the identification of microbes but also linking of functions to species, a feat not achievable by metagenomic techniques. Moreover, it allows the analysis of low abundance species that may be missed in community-based analyses. It has also proved very useful in complementing metagenomics in the assembly and binning of single genomes. With the advent of drastically cheaper and higher throughput sequencing technologies, it is expected that single cell sequencing will become a standard tool in studying the genome and transcriptome of microbial communities. PMID:22154471

  5. Unlocking hidden genomic sequence

    PubMed Central

    Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.

    2004-01-01

    Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs. PMID:14973330

  6. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  7. Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia

    PubMed Central

    Bernal, Johan F.; Donado-Godoy, Pilar; Valencia, María Fernanda; León, Maribel; Gómez, Yolanda; Rodríguez, Fernando; Agarwala, Richa; Landsman, David

    2016-01-01

    Campylobacter coli, along with Campylobacter jejuni, is a major agent of gastroenteritis and acute enterocolitis in humans. We report the whole-genome sequences of two multidrug-resistance C. coli strains, isolated from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and tetracycline. PMID:26988048

  8. Genomic sequencing in clinical trials

    PubMed Central

    2011-01-01

    Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to find its way into clinical trials both nationally and worldwide. We highlight the currently available types of genomic sequencing platforms, outline the advantages and disadvantages of each, and compare first- and next-generation techniques with respect to capabilities, quality, and cost. We describe the current geographical distributions and types of disease conditions in which these technologies are used, and how next-generation sequencing is strategically being incorporated into new and existing studies. Lastly, recent major breakthroughs and the ongoing challenges of using genomic sequencing in clinical research are discussed. PMID:22206293

  9. Decoding the human genome sequence.

    PubMed

    Bentley, D R

    2000-10-01

    The year 2000 is marked by the production of the sequence of the human genome. A 'working draft' of high quality sequence covering 90% of the genome has been determined and a quarter is in finished form, including the first two completed chromosomes. All sequence data from the project is made freely available to the community via the Internet, for further analysis and exploitation. The challenge which lies ahead is to decipher the information. Knowledge of the human genome sequence will enable us to understand how the genetic information determines the development, structure and function of the human body. We will be able to explore how variations within our DNA sequence cause disease, how they affect our interaction with our environment and ultimately to develop new and effective ways to improve human health. PMID:11005789

  10. Integrating sequence, evolution and functional genomics in regulatory genomics

    PubMed Central

    Vingron, Martin; Brazma, Alvis; Coulson, Richard; van Helden, Jacques; Manke, Thomas; Palin, Kimmo; Sand, Olivier; Ukkonen, Esko

    2009-01-01

    With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. PMID:19226437

  11. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  12. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 2 of 2

  13. Poultry Genome Sequences: Progress and Outstanding Challenges

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first build of the chicken genome sequence appeared in March 2004 – the first genome sequence of any animal agriculture species. That sequence was done primarily by whole genome shotgun Sanger sequencing, along with the use of an extensive BAC contig-based physical map to assemble the sequence ...

  14. Sequencing and mapping of the onion genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cost of DNA sequencing continues to decline and, in the near future, it will become reasonable to undertake sequencing of the enormous nuclear genome of onion. We undertook sequencing of expressed and genomic regions of the onion genome to learn about the structure of the onion genome, as well a...

  15. Genome Sequence of Canine Herpesvirus

    PubMed Central

    Papageorgiou, Konstantinos V.; Suárez, Nicolás M.; Wilkie, Gavin S.; McDonald, Michael; Graham, Elizabeth M.; Davison, Andrew J.

    2016-01-01

    Canine herpesvirus is a widespread alphaherpesvirus that causes a fatal haemorrhagic disease of neonatal puppies. We have used high-throughput methods to determine the genome sequences of three viral strains (0194, V777 and V1154) isolated in the United Kingdom between 1985 and 2000. The sequences are very closely related to each other. The canine herpesvirus genome is estimated to be 125 kbp in size and consists of a unique long sequence (97.5 kbp) and a unique short sequence (7.7 kbp) that are each flanked by terminal and internal inverted repeats (38 bp and 10.0 kbp, respectively). The overall nucleotide composition is 31.6% G+C, which is the lowest among the completely sequenced alphaherpesviruses. The genome contains 76 open reading frames predicted to encode functional proteins, all of which have counterparts in other alphaherpesviruses. The availability of the sequences will facilitate future research on the diagnosis and treatment of canine herpesvirus-associated disease. PMID:27213534

  16. Genome Sequence of Spizellomyces punctatus

    PubMed Central

    Russ, Carsten; Lang, B. Franz; Chen, Zehua; Gujja, Sharvari; Shea, Terrance; Zeng, Qiandong; Young, Sarah; Nusbaum, Chad

    2016-01-01

    Spizellomyces punctatus is a basally branching chytrid fungus that is found in the Chytridiomycota phylum. Spizellomyces species are common in soil and of importance in terrestrial ecosystems. Here, we report the genome sequence of S. punctatus, which will facilitate the study of this group of early diverging fungi. PMID:27540072

  17. Meeting Highlights: Genome Sequencing and Biology 2001

    PubMed Central

    2001-01-01

    We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics. PMID:18628920

  18. Sequencing crop genomes: approaches and applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant genome sequencing methodology parrallels the sequencing of the human genome. The first projects were slow and very expensive. BAC by BAC approaches were utilized first and whole-genome shotgun sequencing rapidly replaced that approach. So called 'next generation' technologies such as short rea...

  19. Sequencing Intractable DNA to Close Microbial Genomes

    SciTech Connect

    Hurt, Jr., Richard Ashley; Brown, Steven D; Podar, Mircea; Palumbo, Anthony Vito; Elias, Dwayne A

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  20. Fungal genome sequencing: basic biology to biotechnology.

    PubMed

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research. PMID:25721271

  1. Draft Genome Sequences of Fungus Aspergillus calidoustus.

    PubMed

    Horn, Fabian; Linde, Jörg; Mattern, Derek J; Walther, Grit; Guthke, Reinhard; Scherlach, Kirstin; Martin, Karin; Brakhage, Axel A; Petzke, Lutz; Valiante, Vito

    2016-01-01

    Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504). The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining. PMID:26966204

  2. Draft Genome Sequences of Fungus Aspergillus calidoustus

    PubMed Central

    Horn, Fabian; Linde, Jörg; Mattern, Derek J.; Walther, Grit; Guthke, Reinhard; Scherlach, Kirstin; Martin, Karin; Brakhage, Axel A.; Petzke, Lutz

    2016-01-01

    Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504). The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining. PMID:26966204

  3. Value of a newly sequenced bacterial genome.

    PubMed

    Barbosa, Eudes Gv; Aburjaile, Flavia F; Ramos, Rommel Tj; Carneiro, Adriana R; Le Loir, Yves; Baumbach, Jan; Miyoshi, Anderson; Silva, Artur; Azevedo, Vasco

    2014-05-26

    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information. PMID:24921006

  4. Corrected sequence of the wheat plastid genome.

    PubMed

    Bahieldin, Ahmed; Al-Kordy, Magdy A; Shokry, Ahmed M; Gadalla, Nour O; Al-Hejin, Ahmed M M; Sabir, Jamal S M; Hassan, Sabah M; Al-Ahmadi, Ahlam A; Schwarz, Erika N; Eissa, Hala F; El-Domyati, Fotouh M; Jansen, Robert K

    2014-09-01

    Wheat is the most important cereal in the world in terms of acreage and productivity. We sequenced and assembled the plastid genome of one Egyptian wheat cultivar using next-generation sequence data. The size of the plastid genome is 133,873 bp, which is 672 bp smaller than the published plastid genome of "Chinese Spring" cultivar, due mainly to the presence of three sequences from the rice plastid genome. The difference in size between the previously published wheat plastid genome and the sequence reported here is due to contamination of the published genome with rice plastid DNA, most of which is present in three sequences of 332, 131 and 131 bp. The corrected plastid genome of wheat has been submitted to GenBank (accession number KJ592713) and can be used in future comparisons. PMID:25242688

  5. Real-time, portable genome sequencing for Ebola surveillance.

    PubMed

    Quick, Joshua; Loman, Nicholas J; Duraffour, Sophie; Simpson, Jared T; Severi, Ettore; Cowley, Lauren; Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan H J; Becker-Ziaja, Beate; Boettcher, Jan Peter; Cabeza-Cabrerizo, Mar; Camino-Sánchez, Álvaro; Carter, Lisa L; Doerrbecker, Juliane; Enkirch, Theresa; García-Dorival, Isabel; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigael; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallasch, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Y; Sachse, Andreas; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Racine, Trina; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N'Faly; Williams, Cecelia V; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Frank; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, James; Rachwal, Phillip; Turner, Daniel J; Pollakis, Georgios; Hiscox, Julian A; Matthews, David A; O'Shea, Matthew K; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Wölfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A; Koivogui, Lamine; Diallo, Boubacar; Keïta, Sakoba; Rambaut, Andrew; Formenty, Pierre; Günther, Stephan; Carroll, Miles W

    2016-02-11

    The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks. PMID:26840485

  6. The fungal genome initiative and lessons learned from genome sequencing.

    PubMed

    Cuomo, Christina A; Birren, Bruce W

    2010-01-01

    The sequence of Saccharomyces cerevisiae enabled systematic genome-wide experimental approaches, demonstrating the power of having the complete genome of an organism. The rapid impact of these methods on research in yeast mobilized an effort to expand genomic resources for other fungi. The "fungal genome initiative" represents an organized genome sequencing effort to promote comparative and evolutionary studies across the fungal kingdom. Through such an approach, scientists can not only better understand specific organisms but also illuminate the shared and unique aspects of fungal biology that underlie the importance of fungi in biomedical research, health, food production, and industry. To date, assembled genomes for over 100 fungi are available in public databases, and many more sequencing projects are underway. Here, we discuss both examples of findings from comparative analysis of fungal sequences, with a specific emphasis on yeast genomes, and on the analytical approaches taken to mine fungal genomes. New sequencing methods are accelerating comparative studies of fungi by reducing the cost and difficulty of sequencing. This has driven more common use of sequencing applications, such as to study genome-wide variation in populations or to deeply profile RNA transcripts. These and further technological innovations will continue to be piloted in yeasts and other fungi, and will expand the applications of sequencing to study fungal biology. PMID:20946837

  7. Real-time, portable genome sequencing for Ebola surveillance

    PubMed Central

    Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan HJ; Becker-Ziaja, Beate; Boettcher, Jan-Peter; Cabeza-Cabrerizo, Mar; Camino-Sanchez, Alvaro; Carter, Lisa L.; Doerrbecker, Juiliane; Enkirch, Theresa; Dorival, Isabel Graciela García; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigail; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallash, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Yasmin; Sachse, Andrea; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Trina, Racine; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N’Faly; Williams, Cecelia V.; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Franck; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, Jamie; Rachwal, Philip; Turner, Daniel; Pollakis, Georgios; Hiscox, Julian A.; Matthews, David A.; O’Shea, Matthew K.; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Woelfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A.; Koivogui, Lamine; Diallo, Boubacar; Keita, Sakoba; Rambaut, Andrew; Formenty, Pierre; Gunther, Stephan; Carroll, Miles W.

    2016-01-01

    The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths 1. Genome sequencing in viral outbreaks is desirable in order to characterize the infectious agent to determine its evolutionary rate, signatures of host adaptation, identification and monitoring of diagnostic targets and responses to vaccines and treatments. The Ebola virus genome (EBOV) substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 to 1.42 × 10−3 mutations per site per year. This is equivalent to 16 to 27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic 2-7. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought-after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions 8. Genomic surveillance during the epidemic has been sporadic due to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities 9. In order to address this problem, we devised a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. Here we present sequence data and analysis of 142 Ebola virus (EBOV) samples collected during the period March to October 2015. We were able to generate results in less than 24 hours after receiving an Ebola positive sample, with the sequencing process taking as little as 15-60 minutes. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks. PMID:26840485

  8. Atypical regions in large genomic DNA sequences

    SciTech Connect

    Scherer, S. |; McPeek, M.S.; Speed, T.P.

    1994-07-19

    Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. The authors describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of >1000 nt and human sequences of >10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. The authors consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

  9. Towards a reference pecan genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cost of generating DNA sequence data has declined dramatically over the previous 15 years as a result of the Human Genome Project and the potential applications of genome sequencing for human medicine. This cost reduction has generated renewed interest among crop breeding scientists in applying...

  10. Genome sequence of Lactobacillus rhamnosus ATCC 8530.

    PubMed

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

    2012-02-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences. PMID:22247527

  11. Genome Sequence of Gordonia Phage Yvonnetastic.

    PubMed

    Pope, Welkin H; Bandyopadhyay, Anshika; Carlton, Meghan L; Kane, Meghan T; Panchal, Niyati J; Pham, Yvonne C; Reynolds, Zachary J; Sapienza, Michael S; German, Brian A; McDonnell, Jill E; Schafer, Claire E; Yu, Victor J; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Gordonia bacteriophage Yvonnetastic was isolated from soil in Pittsburgh, PA, using Gordonia terrae 3612 as a host. Yvonnetastic has siphoviral morphology and a genome of 98,136 bp, with 198 predicted protein-coding genes and five tRNA genes. Yvonnetastic does not share substantial sequence similarity with other sequenced bacteriophage genomes. PMID:27389265

  12. Genome Sequence of Gordonia Phage Yvonnetastic

    PubMed Central

    Bandyopadhyay, Anshika; Carlton, Meghan L.; Kane, Meghan T.; Panchal, Niyati J.; Pham, Yvonne C.; Reynolds, Zachary J.; Sapienza, Michael S.; German, Brian A.; McDonnell, Jill E.; Schafer, Claire E.; Yu, Victor J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Gordonia bacteriophage Yvonnetastic was isolated from soil in Pittsburgh, PA, using Gordonia terrae 3612 as a host. Yvonnetastic has siphoviral morphology and a genome of 98,136 bp, with 198 predicted protein-coding genes and five tRNA genes. Yvonnetastic does not share substantial sequence similarity with other sequenced bacteriophage genomes. PMID:27389265

  13. Next generation sequencing of viral RNA genomes

    PubMed Central

    2013-01-01

    Background With the advent of Next Generation Sequencing (NGS) technologies, the ability to generate large amounts of sequence data has revolutionized the genomics field. Most RNA viruses have relatively small genomes in comparison to other organisms and as such, would appear to be an obvious success story for the use of NGS technologies. However, due to the relatively low abundance of viral RNA in relation to host RNA, RNA viruses have proved relatively difficult to sequence using NGS technologies. Here we detail a simple, robust methodology, without the use of ultra-centrifugation, filtration or viral enrichment protocols, to prepare RNA from diagnostic clinical tissue samples, cell monolayers and tissue culture supernatant, for subsequent sequencing on the Roche 454 platform. Results As representative RNA viruses, full genome sequence was successfully obtained from known lyssaviruses belonging to recognized species and a novel lyssavirus species using these protocols and assembling the reads using de novo algorithms. Furthermore, genome sequences were generated from considerably less than 200 ng RNA, indicating that manufacturers’ minimum template guidance is conservative. In addition to obtaining genome consensus sequence, a high proportion of SNPs (Single Nucleotide Polymorphisms) were identified in the majority of samples analyzed. Conclusions The approaches reported clearly facilitate successful full genome lyssavirus sequencing and can be universally applied to discovering and obtaining consensus genome sequences of RNA viruses from a variety of sources. PMID:23822119

  14. Human Genome Sequencing in Health and Disease

    PubMed Central

    Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

    2013-01-01

    Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

  15. The genome sequence of parrot bornavirus 5.

    PubMed

    Guo, Jianhua; Tizard, Ian

    2015-12-01

    Although several new avian bornaviruses have recently been described, information on their evolution, virulence, and sequence are often limited. Here we report the complete genome sequence of parrot bornavirus 5 (PaBV-5) isolated from a case of proventricular dilatation disease in a Palm cockatoo (Probosciger aterrimus). The complete genome consists of 8842 nucleotides with distinct 5' and 3' end sequences. This virus shares nucleotide sequence identities of 69-74 % with other bornaviruses in the genomic regions excluding the 5' and 3' terminal sequences. Phylogenetic analysis based on the genomic regions demonstrated this new isolate is an isolated branch within the clade that includes the aquatic bird bornaviruses and the passerine bornaviruses. Based on phylogenetic analyses and its low nucleotide sequence identities with other bornavirus, we support the proposal that PaBV-5 be assigned to a new bornavirus species:- Psittaciform 2 bornavirus. PMID:26403158

  16. Translational genomics for plant breeding with the genome sequence explosion.

    PubMed

    Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha

    2016-04-01

    The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies. PMID:26269219

  17. Sequence Maneuverer: tool for sequence extraction from genomes

    PubMed Central

    Yasmin, Tayyaba; Rehman, Inayat Ur; Ansari, Adnan Ahmad; liaqat, Khurrum; khan, Muhammad Irfan

    2012-01-01

    The availability of genomic sequences of many organisms has opened new challenges in many aspects particularly in terms of genome analysis. Sequence extraction is a vital step and many tools have been developed to solve this issue. These tools are available publically but have limitations with reference to the sequence extraction, length of the sequence to be extracted, organism specificity and lack of user friendly interface. We have developed a java based software package having three modules which can be used independently or sequentially. The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism. The results are crosschecked by published data. Availability URL 1: http://ww3.comsats.edu.pk/bio/ResearchProjects.aspx URL 2: http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx PMID:23275734

  18. Genome Sequencing and Analysis Conference IV

    SciTech Connect

    Not Available

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  19. Genomic sequencing of Pleistocene cave bears

    SciTech Connect

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  20. Assessing inhomogeneities in bacterial long genomic sequences

    SciTech Connect

    Karlin, S.

    1997-12-01

    Several complete prokaryotic and eukaryotic genomes are already at hand (S. cerevisiae, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, sp.) and many are forthcoming (e.g., E. coli, H, pylori, C. elegans). The comparative analysis of genomes generally strives to identify genes and characterize function/structure relationships inferred mostly via amino acid sequence comparisons. We describe concisely methods for comparing genomes (or long contigs) emphasizing sequence features other than gene comparisons. These center on the following measures of genomic organization and sequence heterogeneity: (i) compositional biases of short oligonucleotides; (ii) dinucleotide relative abundance distances within and between genomes; (iii) rare and frequent word (oligonucleotide) determinations and their distributional properties; (iv) r-scan statistics assessing clustering, overdispersion, or excessive evenness of various marker arrays; and (v) characterizations of repeat structures in the genome. 20 refs., 3 figs.

  1. The genome sequence of Drosophila melanogaster.

    SciTech Connect

    2000-03-24

    The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the {approximately}120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes {approximately}13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

  2. Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes

    PubMed Central

    Barthelson, Roger; McFarlin, Adam J.; Rounsley, Steven D.; Young, Sarah

    2011-01-01

    Background Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. Methodology/Principal Findings For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. Conclusions/Significance Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly further. PMID:22174807

  3. Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

    PubMed Central

    Zhang, Shaokang; Yin, Yanlong; Jones, Marcus B.; Zhang, Zhenzhen; Deatherage Kaiser, Brooke L.; Dinsmore, Blake A.; Fitzgerald, Collette; Fields, Patricia I.

    2015-01-01

    Serotyping forms the basis of national and international surveillance networks for Salmonella, one of the most prevalent foodborne pathogens worldwide (1–3). Public health microbiology is currently being transformed by whole-genome sequencing (WGS), which opens the door to serotype determination using WGS data. SeqSero (www.denglab.info/SeqSero) is a novel Web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing (i) raw reads from genomes of 308 Salmonella isolates of known serotype; (ii) raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and (iii) 354 other publicly available draft or complete Salmonella genomes. We also demonstrated Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization. PMID:25762776

  4. Sequencing and Analysis of Neanderthal Genomic DNA

    PubMed Central

    Noonan, James P.; Coop, Graham; Kudaravalli, Sridhar; Smith, Doug; Krause, Johannes; Alessi, Joe; Chen, Feng; Platt, Darren; Pääbo, Svante; Pritchard, Jonathan K.; Rubin, Edward M.

    2008-01-01

    Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor ~706,000 years ago, and that the human and Neanderthal ancestral populations split ~370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics. PMID:17110569

  5. Microbial species delineation using whole genome sequences

    SciTech Connect

    Kyrpides, Nikos; Mukherjee, Supratim; Ivanova, Natalia; Mavrommatics, Kostas; Pati, Amrita; Konstantinidis, Konstantinos

    2014-10-20

    Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both phenotypic traits and sequence information of phylogenetic marker genes. With thousands of genomes being sequenced every year, an automated, uniform and scalable approach exploiting the rich genomic information in whole genome sequences is desired, at least for the initial assignment of species to an organism. We have evaluated pairwise genome-wide Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 genomes using our fast implementation of the computation, identifying robust and widely applicable hard cut-offs for species assignments based on AF and gANI. Using these cutoffs, we generated stable species-level clusters of organisms, which enabled the identification of several species mis-assignments and facilitated the assignment of species for organisms without species definitions.

  6. Genome sequence of Coxiella burnetii strain Namibia

    PubMed Central

    2014-01-01

    We present the whole genome sequence and annotation of the Coxiella burnetii strain Namibia. This strain was isolated from an aborting goat in 1991 in Windhoek, Namibia. The plasmid type QpRS was confirmed in our work. Further genomic typing placed the strain into a unique genomic group. The genome sequence is 2,101,438 bp long and contains 1,979 protein-coding and 51 RNA genes, including one rRNA operon. To overcome the poor yield from cell culture systems, an additional DNA enrichment with whole genome amplification (WGA) methods was applied. We describe a bioinformatics pipeline for improved genome assembly including several filters with a special focus on WGA characteristics. PMID:25593636

  7. Complementary DNA sequencing: Expressed sequence tags and human genome project

    SciTech Connect

    Adams, M.D.; Kelley, J.M.; Gocayne, J.D.; Dubnick, M.; Wu, A.; Olde, B.; Moreno, R.F.; Kerlavage, A.R.; McCombie, W.R.; Venter, J.C. ); Polymeropoulos, M.H.; Hong Xiao; Merril, C.R. )

    1991-06-21

    Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.

  8. Automated correction of genome sequence errors

    PubMed Central

    Gajer, Pawel; Schatz, Michael; Salzberg, Steven L.

    2004-01-01

    By using information from an assembly of a genome, a new program called AutoEditor significantly improves base calling accuracy over that achieved by previous algorithms. This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery. We describe the algorithm and its application in a large set of recent genome sequencing projects. The number of erroneous base calls in these projects was reduced by 80%. In an analysis of over one million corrections, we found that AutoEditor made just one error per 8828 corrections. By substantially increasing the accuracy of base calling, AutoEditor can dramatically accelerate the process of finishing genomes, which involves closing all gaps and ensuring minimum quality standards for the final sequence. It also greatly improves our ability to discover single nucleotide polymorphisms (SNPs) between closely related strains and isolates of the same species. PMID:14744981

  9. Complete genome sequence of tobacco mosqueado virus.

    PubMed

    Blawid, Rosana; Rodrigues, Kelly Barreto; de Moraes Rêgo, Camila; Inoue-Nagata, Alice K; Nagata, Tatsuya

    2016-09-01

    We describe the genomic characteristics of a new potyvirus isolated from tobacco plants showing mottling ("mosqueado" in Portuguese) in southern Brazil. The complete genomic sequence consists of 9896 nucleotides, without the poly(A) tail, and shares the highest pairwise nucleotide sequence identities of 68.5 % with pepper yellow mosaic virus and 68.2 % with Brugmansia mosaic virus isolate D437. These identity values are below the level of 76.0 % used as a criterion for species demarcation in the genus Potyvirus based on the complete genome sequence. The viral genomic organization and sequence comparison thus suggest that this virus, tentatively named "tobacco mosqueado virus" (TMosqV), represents a new potyvirus species. PMID:27368991

  10. Genome sequence and analysis of Lactobacillus helveticus

    PubMed Central

    Cremonesi, Paola; Chessa, Stefania; Castiglioni, Bianca

    2013-01-01

    The microbiological characterization of lactobacilli is historically well developed, but the genomic analysis is recent. Because of the widespread use of Lactobacillus helveticus in cheese technology, information concerning the heterogeneity in this species is accumulating rapidly. Recently, the genome of five L. helveticus strains was sequenced to completion and compared with other genomically characterized lactobacilli. The genomic analysis of the first sequenced strain, L. helveticus DPC 4571, isolated from cheese and selected for its characteristics of rapid lysis and high proteolytic activity, has revealed a plethora of genes with industrial potential including those responsible for key metabolic functions such as proteolysis, lipolysis, and cell lysis. These genes and their derived enzymes can facilitate the production of cheese and cheese derivatives with potential for use as ingredients in consumer foods. In addition, L. helveticus has the potential to produce peptides with a biological function, such as angiotensin converting enzyme (ACE) inhibitory activity, in fermented dairy products, demonstrating the therapeutic value of this species. A most intriguing feature of the genome of L. helveticus is the remarkable similarity in gene content with many intestinal lactobacilli. Comparative genomics has allowed the identification of key gene sets that facilitate a variety of lifestyles including adaptation to food matrices or the gastrointestinal tract. As genome sequence and functional genomic information continues to explode, key features of the genomes of L. helveticus strains continue to be discovered, answering many questions but also raising many new ones. PMID:23335916

  11. Sequencing and comparing whole mitochondrial genomes ofanimals

    SciTech Connect

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  12. Complete genome sequence of arracacha mottle virus.

    PubMed

    Orílio, Anelise F; Lucinda, Natalia; Dusi, André N; Nagata, Tatsuya; Inoue-Nagata, Alice K

    2013-01-01

    Arracacha mottle virus (AMoV) is the only potyvirus reported to infect arracacha (Arracacia xanthorrhiza) in Brazil. Here, the complete genome sequence of an isolate of AMoV was determined to be 9,630 nucleotides in length, excluding the 3' poly-A tail, and encoding a polyprotein of 3,135 amino acids and a putative P3N-PIPO protein. Its genomic organization is typical of a member of the genus Potyvirus, containing all conserved motifs. Its full genome sequence shared 56.2 % nucleotide identity with sunflower chlorotic mottle virus and verbena virus Y, the most closely related viruses. PMID:23001696

  13. A Workshop Report on Wheat Genome Sequencing

    PubMed Central

    Gill, Bikram S.; Appels, Rudi; Botha-Oberholster, Anna-Maria; Buell, C. Robin; Bennetzen, Jeffrey L.; Chalhoub, Boulos; Chumley, Forrest; Dvořák, Jan; Iwanaga, Masaru; Keller, Beat; Li, Wanlong; McCombie, W. Richard; Ogihara, Yasunari; Quetier, Francis; Sasaki, Takuji

    2004-01-01

    Sponsored by the National Science Foundation and the U.S. Department of Agriculture, a wheat genome sequencing workshop was held November 10–11, 2003, in Washington, DC. It brought together 63 scientists of diverse research interests and institutions, including 45 from the United States and 18 from a dozen foreign countries (see list of participants at http://www.ksu.edu/igrow). The objectives of the workshop were to discuss the status of wheat genomics, obtain feedback from ongoing genome sequencing projects, and develop strategies for sequencing the wheat genome. The purpose of this report is to convey the information discussed at the workshop and provide the basis for an ongoing dialogue, bringing forth comments and suggestions from the genetics community. PMID:15514080

  14. Complete Genome Sequencing of Trivittatus virus

    PubMed Central

    Groseth, Allison; Vine, Veronica; Weisend, Carla; Ebihara, Hideki

    2015-01-01

    Trivittatus virus (family Bunyaviridae, genus Orthobunyavirus) represents an important genetic intermediate between the California encephalitis group, and Bwamba/Pongola and Nyando groups. Here, we report the first complete genome sequence of the prototype (Eklund) strain, isolated in 1948, which interestingly shows only few differences compared to partial sequences of modern strains. PMID:26212363

  15. Draft Genome Sequence of Goose Dicistrovirus

    PubMed Central

    Jerome, Keith R.

    2016-01-01

    We report the draft genome sequence of goose dicistrovirus assembled from the filtered feces of a Canadian goose from South Lake Union in Seattle, Washington. The 9.1-kb dicistronic RNA virus falls within the family Dicistroviridae; however, it shares <33% translated amino acid sequence within the nonstructural open reading frame (ORF) from aparavirus or cripavirus. PMID:26941149

  16. Complete Genome Sequences of 63 Mycobacteriophages

    PubMed Central

    2013-01-01

    Mycobacteriophages are viruses that infect mycobacterial hosts. The current collection of sequenced mycobacteriophages—all isolated on a single host strain, Mycobacterium smegmatis mc2155, reveals substantial genetic diversity. The complete genome sequences of 63 newly isolated mycobacteriophages expand the resolution of our understanding of phage diversity. PMID:24285655

  17. Genome Sequence of Pseudomonas chlororaphis Strain 189

    PubMed Central

    Town, Jennifer; Audy, Patrice; Boyetchko, Susan M.

    2016-01-01

    Pseudomonas chlororaphis strain 189 is a potent inhibitor of the growth of the potato pathogen Phytophthora infestans. We determined the complete, finished sequence of the 6.8-Mbp genome of this strain, consisting of a single contiguous molecule. Strain 189 is closely related to previously sequenced strains of P. chlororaphis. PMID:27340063

  18. Draft Genome Sequence of Goose Dicistrovirus.

    PubMed

    Greninger, Alexander L; Jerome, Keith R

    2016-01-01

    We report the draft genome sequence of goose dicistrovirus assembled from the filtered feces of a Canadian goose from South Lake Union in Seattle, Washington. The 9.1-kb dicistronic RNA virus falls within the family Dicistroviridae; however, it shares <33% translated amino acid sequence within the nonstructural open reading frame (ORF) from aparavirus or cripavirus. PMID:26941149

  19. Global Alignment System for Large Genomic Sequencing

    Energy Science and Technology Software Center (ESTSC)

    2002-03-01

    AVID is a global alignment system tailored for the alignment of large genomic sequences up to megabases in length. Features include the possibility of one sequence being in draft form, fast alignment, robustness and accuracy. The method is an anchor based alignment using maximal matches derived from suffix trees.

  20. Genomic sequence analysis tools: a user's guide.

    PubMed

    Fortna, A; Gardiner, K

    2001-03-01

    The wealth of information from various genome sequencing projects provides the biologist with a new perspective from which to analyze, and design experiments with, mammalian systems. The complexity of the information, however, requires new software tools, and numerous such tools are now available. Which type and which specific system is most effective depends, in part, upon how much sequence is to be analyzed and with what level of experimental support. Here we survey a number of mammalian genomic sequence analysis systems with respect to the data they provide and the ease of their use. The hope is to aid the experimental biologist in choosing the most appropriate tool for their analyses. PMID:11226611

  1. Genome Sequence of Mycobacteriophage Cabrinians

    PubMed Central

    Chudoff, Dylan; Conboy, Andrew; Conboy, Danielle; Atoulelou, Mireille; Hasan, Sakina; Martinez, Alexandria; Mastrando, Jessica; Roy, Renoy; Schmidt, Robert; Sheed, Kabreeze; Smith, Jewel; Sperratore, Morgan; Struga, Rexhina; Starr, Katelyn; Suppi, Regina; Uguru, Ugo; Terry, Katrina; Villafuerte, Rosendo; Yuan, Vanessa

    2016-01-01

    Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both Mycobacterium phlei and Mycobacterium smegmatis and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F. PMID:26847904

  2. Genome Sequence of Mycobacteriophage Cabrinians.

    PubMed

    Chudoff, Dylan; Conboy, Andrew; Conboy, Danielle; Atoulelou, Mireille; Hasan, Sakina; Martinez, Alexandria; Mastrando, Jessica; Roy, Renoy; Schmidt, Robert; Sheed, Kabreeze; Smith, Jewel; Sperratore, Morgan; Struga, Rexhina; Starr, Katelyn; Suppi, Regina; Uguru, Ugo; Terry, Katrina; Villafuerte, Rosendo; Yuan, Vanessa; Dunbar, David

    2016-01-01

    Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both Mycobacterium phlei and Mycobacterium smegmatis and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F. PMID:26847904

  3. Genome Sequence of the Palaeopolyploid soybean

    SciTech Connect

    Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; Ma, Jianxin; Mitros, Therese; Nelson, William; Hyten, David L.; Song, Qijian; Thelen, Jay J.; Cheng, Jianlin; Xu, Dong; Hellsten, Uffe; May, Gregory D.; Yu, Yeisoo; Sakura, Tetsuya; Umezawa, Taishi; Bhattacharyya, Madan K.; Sandhu, Devinder; Valliyodan, Babu; Lindquist, Erika; Peto, Myron; Grant, David; Shu, Shengqiang; Goodstein, David; Barry, Kerrie; Futrell-Griggs, Montona; Abernathy, Brian; Du, Jianchang; Tian, Zhixi; Zhu, Liucun; Gill, Navdeep; Joshi, Trupti; Libault, Marc; Sethuraman, Anand; Zhang, Xue-Cheng; Shinozaki, Kazuo; Nguyen, Henry T.; Wing, Rod A.; Cregan, Perry; Specht, James; Grimwood, Jane; Rokhsar, Dan; Stacey, Gary; Shoemaker, Randy C.; Jackson, Scott A.

    2009-08-03

    Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70percent more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78percent of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75percent of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

  4. Rhipicephalus (Boophilus) microplus strain Deutsch, whole genome shotgun sequencing project first submission of genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence difficult. Cot filtration/selection techniques were used to reduce the repetitive fraction of the tick genome and enrich for the fraction of DNA with gene-containing regions. The Cot-selected ...

  5. Sequencing and analysis of a genomic fragment provide an insight into the Dunaliella viridis genomic sequence.

    PubMed

    Sun, Xiao-Ming; Tang, Yuan-Ping; Meng, Xiang-Zong; Zhang, Wen-Wen; Li, Shan; Deng, Zhi-Rui; Xu, Zheng-Kai; Song, Ren-Tao

    2006-11-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)(n) type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features. PMID:17091199

  6. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    PubMed

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541

  7. Accelerating Genome Sequencing 100X with FPGAs

    SciTech Connect

    Storaasli, Olaf O; Strenski, Dave

    2007-01-01

    The performance of two Cray XD1 systems with Virtex-II Pro 50 and Virtex-4 LX160 FPGAs was evaluated using the FASTA computational biology program for human genome (DNA and protein) sequence comparisons. FPGA speedups of 50X (Virtex-II Pro 50) and 100X (Virtex-4 LX160) over a 2.2 GHz Opteron were obtained. FPGA coding issues for human genome data are described.

  8. Microbial species delineation using whole genome sequences

    PubMed Central

    Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T.; Mavrommatis, Kostas; Kyrpides, Nikos C.; Pati, Amrita

    2015-01-01

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. PMID:26150420

  9. Sequencing the AML Genome, Transcriptome, and Epigenome

    PubMed Central

    Mardis, Elaine R.

    2014-01-01

    Leukemia is a disease that develops as a result of changes in the genomes of hematopoietic cells, a fact first appreciated by microscopic examination of the bone marrow cell chromosomes of affected patients. These studies revealed that specific subtypes of leukemia diagnosis correlated with specific chromosomal abnormalities, such as the t(15;17) of acute promyelocytic leukemia1 and the t(9;22) of chronic myeloid leukemia2. Over time, our genomic characterization of hematologic malignancies has moved beyond the resolution of the microscope to that of individual nucleotides in the analysis of whole genome sequencing data using state-of-the-art massively parallel sequencing (MPS) instruments and algorithmic analyses of the resulting data. In addition to studying the genomic sequence alterations that occur in patient’s genomes, these same instruments can decode the methylation landscape of the leukemia genome and the resulting RNA expression landscape of the leukemia transcriptome. Broad correlative analyses can then integrate these three data types to better inform researchers and clinicians about the biology of individual acute myeloid leukemia (AML) cases, facilitating improvements in care and prognosis. PMID:25311738

  10. Sorghum genome sequencing by methylation filtration.

    PubMed

    Bedell, Joseph A; Budiman, Muhammad A; Nunberg, Andrew; Citek, Robert W; Robbins, Dan; Jones, Joshua; Flick, Elizabeth; Rholfing, Theresa; Fries, Jason; Bradford, Kourtney; McMenamy, Jennifer; Smith, Michael; Holeman, Heather; Roe, Bruce A; Wiley, Graham; Korf, Ian F; Rabinowicz, Pablo D; Lakey, Nathan; McCombie, W Richard; Jeddeloh, Jeffrey A; Martienssen, Robert A

    2005-01-01

    Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis. PMID:15660154

  11. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

    PubMed

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-01

    Genetic analyses play a central role in infectious disease research. Massively parallelized "mechanical cloning" and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure--from nucleic acid extraction to sequencing--should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping. PMID:26751471

  12. An International Plan to Sequence the Onion Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cost of DNA sequencing continues to decline and, in the near future, it will become reasonable to undertake sequencing of the enormous nuclear genome of onion. We undertook sequencing of expressed and genomic regions of the onion genome to learn about the structure of the onion genome, as well a...

  13. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    PubMed Central

    Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W.; Aarestrup, Frank M.; Lund, Ole

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the “gold standard” of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST. PMID:22238442

  14. Multilocus sequence typing of total-genome-sequenced bacteria.

    PubMed

    Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

    2012-04-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST. PMID:22238442

  15. Mapping and sequencing the human genome

    SciTech Connect

    1988-01-01

    Numerous meetings have been held and a debate has developed in the biological community over the merits of mapping and sequencing the human genome. In response a committee to examine the desirability and feasibility of mapping and sequencing the human genome was formed to suggest options for implementing the project. The committee asked many questions. Should the analysis of the human genome be left entirely to the traditionally uncoordinated, but highly successful, support systems that fund the vast majority of biomedical research. Or should a more focused and coordinated additional support system be developed that is limited to encouraging and facilitating the mapping and eventual sequencing of the human genome. If so, how can this be done without distorting the broader goals of biological research that are crucial for any understanding of the data generated in such a human genome project. As the committee became better informed on the many relevant issues, the opinions of its members coalesced, producing a shared consensus of what should be done. This report reflects that consensus.

  16. Mapping and Sequencing the Human Genome

    DOE R&D Accomplishments Database

    1988-01-01

    Numerous meetings have been held and a debate has developed in the biological community over the merits of mapping and sequencing the human genome. In response a committee to examine the desirability and feasibility of mapping and sequencing the human genome was formed to suggest options for implementing the project. The committee asked many questions. Should the analysis of the human genome be left entirely to the traditionally uncoordinated, but highly successful, support systems that fund the vast majority of biomedical research. Or should a more focused and coordinated additional support system be developed that is limited to encouraging and facilitating the mapping and eventual sequencing of the human genome. If so, how can this be done without distorting the broader goals of biological research that are crucial for any understanding of the data generated in such a human genome project. As the committee became better informed on the many relevant issues, the opinions of its members coalesced, producing a shared consensus of what should be done. This report reflects that consensus.

  17. Genome Sequence of Gordonia Phage Emalyn

    PubMed Central

    Guido, Madeline J.; Iyengar, Pragnya; Nigra, Jonathan T.; Serbin, Matthew B.; Kasturiarachi, Naomi S.; Pressimone, Catherine A.; Schiebel, Johnathon G.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages. PMID:27516499

  18. Genome Sequence of Gordonia Phage Emalyn.

    PubMed

    Pope, Welkin H; Guido, Madeline J; Iyengar, Pragnya; Nigra, Jonathan T; Serbin, Matthew B; Kasturiarachi, Naomi S; Pressimone, Catherine A; Schiebel, Johnathon G; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages. PMID:27516499

  19. Genome sequence of Lactobacillus amylovorus GRL1112.

    PubMed

    Kant, Ravi; Paulin, Lars; Alatalo, Edward; de Vos, Willem M; Palva, Airi

    2011-02-01

    Lactobacillus amylovorus is a common member of the normal gastrointestinal tract (GIT) microbiota in pigs. Here, we report the genome sequence of L. amylovorus GRL1112, a porcine feces isolate displaying strong adherence to the pig intestinal epithelial cells. The strain is of interest, as it is a potential probiotic bacterium. PMID:21131492

  20. Complete Genome Sequences of 61 Mycobacteriophages.

    PubMed

    Hatfull, Graham F

    2016-01-01

    Mycobacteriophages-viruses of mycobacteria-provide insights into viral diversity and evolution as well as numerous tools for genetic dissection of Mycobacterium tuberculosis Here we report the complete genome sequences of 61 mycobacteriophages newly isolated from environmental samples using Mycobacterium smegmatis mc(2)155 that expand our understanding of phage diversity. PMID:27389257

  1. Genome Sequence of Corynebacterium ulcerans Strain 210932

    PubMed Central

    Viana, Marcus Vinicius Canário; de Jesus Benevides, Leandro; Batista Mariano, Diego Cesar; de Souza Rocha, Flávia; Bagano Vilas Boas, Priscilla Carolinne; Folador, Edson Luiz; Pereira, Felipe Luiz; Alves Dorella, Fernanda; Gomes Leal, Carlos Augusto; Fiorini de Carvalho, Alex; Silva, Artur; de Castro Soares, Siomar; Pereira Figueiredo, Henrique Cesar; Guimarães, Luis Carlos

    2014-01-01

    In this work, we present the complete genome sequence of Corynebacterium ulcerans strain 210932, isolated from a human. The species is an emergent pathogen that infects a variety of wild and domesticated animals and humans. It is associated with a growing number of cases of a diphtheria-like disease around the world. PMID:25428977

  2. Complete Genome Sequences of 61 Mycobacteriophages

    PubMed Central

    2016-01-01

    Mycobacteriophages—viruses of mycobacteria—provide insights into viral diversity and evolution as well as numerous tools for genetic dissection of Mycobacterium tuberculosis. Here we report the complete genome sequences of 61 mycobacteriophages newly isolated from environmental samples using Mycobacterium smegmatis mc2155 that expand our understanding of phage diversity. PMID:27389257

  3. Whole genome sequences of four Brucella strains.

    PubMed

    Ding, Jiabo; Pan, Yuanlong; Jiang, Hai; Cheng, Junsheng; Liu, Taotao; Qin, Nan; Yang, Yi; Cui, Buyun; Chen, Chen; Liu, Cuihua; Mao, Kairong; Zhu, Baoli

    2011-07-01

    Brucella melitensis and Brucella suis are intracellular pathogens of livestock and humans. Here we report four genome sequences, those of the virulent strain B. melitensis M28-12 and vaccine strains B. melitensis M5 and M111 and B. suis S2, which show different virulences and pathogenicities, which will help to design a more effective brucellosis vaccine. PMID:21602346

  4. Draft Genome Sequence of Virgibacillus halodenitrificans 1806

    PubMed Central

    Lee, Sang-Jae; Lee, Yong-Jik; Jeong, Haeyoung; Lee, Sang Jun; Lee, Han-Seung; Pan, Jae-Gu

    2012-01-01

    Virgibacillus halodenitrificans 1806 is an endospore-forming halophilic bacterium isolated from salterns in Korea. Here, we report the draft genome sequence of V. halodenitrificans 1806, which may reveal the molecular basis of osmoadaptation and insights into carbon and anaerobic metabolism in moderate halophiles. PMID:23105070

  5. Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these s...

  6. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

    PubMed Central

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-01

    Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure—from nucleic acid extraction to sequencing—should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping. PMID:26751471

  7. A Pan-HIV Strategy for Complete Genome Sequencing.

    PubMed

    Berg, Michael G; Yamaguchi, Julie; Alessandri-Gradt, Elodie; Tell, Robert W; Plantier, Jean-Christophe; Brennan, Catherine A

    2016-04-01

    Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,switchingmechanismat 5' end ofRNAtranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance. PMID:26699702

  8. Gambling on a shortcut to genome sequencing

    SciTech Connect

    Roberts, L.

    1991-06-21

    Almost from the start of the Human Genome Project, a debate has been raging over whether to sequence the entire human genome, all 3 billion bases, or just the genes - a mere 2% or 3% of the genome, and by far the most interesting part. In England, Sydney Brenner convinced the Medical Research Council (MRC) to start with the expressed genes, or complementary DNAs. But the US stance has been that the entire sequence is essential if we are to understand the blueprint of man. Craig Venter of the National Institute of Neurological Disorders and Stroke says that focusing on the expressed genes may be even more useful than expected. His strategy involves randomly selecting clones from cDNA libraries which theoretically contain all the genes that are switched on at a particular time in a particular tissue. Then the researchers sequence just a short stretch of each clone, about 400 to 500 bases, to create can expressed sequence tag or EST. The sequences of these ESTs are then stored in a database. Using that information, other researchers can then recreate that EST by using polymerase chain reaction techniques.

  9. Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

    PubMed

    Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

    2016-08-15

    Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities. PMID:27006240

  10. Agaricus bisporus genome sequence: a commentary.

    PubMed

    Kerrigan, Richard W; Challen, Michael P; Burton, Kerry S

    2013-06-01

    The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, 'humicolous', for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and β-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. PMID:23558250

  11. Comparative Analysis of Genome Sequences with VISTA

    DOE Data Explorer

    Dubchak, Inna

    VISTA is a comprehensive suite of programs and databases developed by and hosted at the Genomics Division of Lawrence Berkeley National Laboratory. They provide information and tools designed to facilitate comparative analysis of genomic sequences. Users have two ways to interact with the suite of applications at the VISTA portal. They can submit their own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. A key menu option is the Enhancer Browser and Database at http://enhancer.lbl.gov/. The VISTA Enhancer Browser is a central resource for experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates. The results of this enhancer screen are provided through this publicly available website. The browser also features relevant results by external contributors and a large collection of additional genome-wide conserved noncoding elements which are candidate enhancer sequences. The LBL developers invite external groups to submit computational predictions of developmental enhancers. As of 10/19/2009 the database contains information on 1109 in vivo tested elements - 508 elements with enhancer activity.

  12. Whole-genome sequencing in bacteriology: state of the art

    PubMed Central

    Dark, Michael J

    2013-01-01

    Over the last ten years, genome sequencing capabilities have expanded exponentially. There have been tremendous advances in sequencing technology, DNA sample preparation, genome assembly, and data analysis. This has led to advances in a number of facets of bacterial genomics, including metagenomics, clinical medicine, bacterial archaeology, and bacterial evolution. This review examines the strengths and weaknesses of techniques in bacterial genome sequencing, upcoming technologies, and assembly techniques, as well as highlighting recent studies that highlight new applications for bacterial genomics. PMID:24143115

  13. Draft Genome Sequence of Mycobacterium brumae ATCC 51384

    PubMed Central

    D'Auria, Giuseppe

    2016-01-01

    Here, we report the draft genome sequence of Mycobacterium brumae type strain ATCC 51384. This is the first draft genome sequence of M. brumae, a nonpathogenic, rapidly growing, nonchromogenic mycobacterium, with immunotherapeutic capacities. PMID:27125480

  14. Whole Genome Sequencing: Cracking the Genetic Code for Foodborne Illness

    MedlinePlus

    ... Consumers Consumer Updates Whole Genome Sequencing: Cracking the Genetic Code for Foodborne Illness Share Tweet Linkedin Pin ... have millions of different genomes, or sequences of genetic code, each as unique as a fingerprint. Get ...

  15. Genome Sequence of Psychrobacter cibarius Strain W1

    PubMed Central

    Raghupathi, Prem K.; Herschend, Jakob; Røder, Henriette L.; Sørensen, Søren J.

    2016-01-01

    Here, we report the draft genome sequence of Psychrobacter cibarius strain W1, which was isolated at a slaughterhouse in Denmark. The 3.63-Mb genome sequence was assembled into 241 contigs. PMID:27231353

  16. Whole genome sequence analysis of Mycobacterium suricattae.

    PubMed

    Dippenaar, Anzaan; Parsons, Sven David Charles; Sampson, Samantha Leigh; van der Merwe, Ruben Gerhard; Drewe, Julian Ashley; Abdallah, Abdallah Musa; Siame, Kabengele Keith; Gey van Pittius, Nicolaas Claudius; van Helden, Paul David; Pain, Arnab; Warren, Robin Mark

    2015-12-01

    Tuberculosis occurs in various mammalian hosts and is caused by a range of different lineages of the Mycobacterium tuberculosis complex (MTBC). A recently described member, Mycobacterium suricattae, causes tuberculosis in meerkats (Suricata suricatta) in Southern Africa and preliminary genetic analysis showed this organism to be closely related to an MTBC pathogen of rock hyraxes (Procavia capensis), the dassie bacillus. Here we make use of whole genome sequencing to describe the evolution of the genome of M. suricattae, including known and novel regions of difference, SNPs and IS6110 insertion sites. We used genome-wide phylogenetic analysis to show that M. suricattae clusters with the chimpanzee bacillus, previously isolated from a chimpanzee (Pan troglodytes) in West Africa. We propose an evolutionary scenario for the Mycobacterium africanum lineage 6 complex, showing the evolutionary relationship of M. africanum and chimpanzee bacillus, and the closely related members M. suricattae, dassie bacillus and Mycobacterium mungi. PMID:26542221

  17. Simple sequence repeats in prokaryotic genomes

    PubMed Central

    Mrázek, Jan; Guo, Xiangxue; Shah, Apurva

    2007-01-01

    Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1–4 bp length, designated LSSR1–4) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5–11 bp length, designated LSSR5–11) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR1–4 are likely maintained by selection. This is consistent with the established role of some LSSR1–4 in enhancing antigenic variance. By contrast, abundance of LSSR5–11 in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed. PMID:17485665

  18. Elucidating population histories using genomic DNA sequences.

    PubMed

    Vigilant, Linda

    2009-04-01

    In 1993, Cliff Jolly suggested that rather than debating species definitions and classifications, energy would be better spent investigating multidimensional patterns of variation and gene flow among populations. Until now, however, genetic studies of wild primate populations have been limited to very small portions of the genome. Access to complete genome sequences of humans, chimpanzees, macaques, and other primates makes it possible to design studies surveying substantial amounts of DNA sequence variation at multiple genetic loci in representatives of closely related but distinct wild primate populations. Such data can be analyzed with new approaches that estimate not only when populations diverged but also the relative amounts and directions of subsequent gene flow. These analyses will reemphasize the difficulty of achieving consistent species and subspecies definitions by revealing the extent of variation in the amount and duration of gene flow accompanying population divergences. PMID:19817223

  19. Complete genome sequence of Piry vesiculovirus.

    PubMed

    de Souza, William Marciel; Acrani, Gustavo Olszanski; Romeiro, Marilia Farignoli; Júnior, Osvaldo Reis; Tolardo, Aline Lavado; de Andrade, Amanda Araújo Serrão; da Silva Gonçalves Vianez Júnior, João Lídio; de Almeida Medeiros, Daniele Barbosa; Nunes, Márcio Roberto Teixeira; Figueiredo, Luiz Tadeu Moraes

    2016-08-01

    Piry virus (PIRYV) is a rhabdovirus (genus Vesiculovirus) and is described as a possible human pathogen, originally isolated from a Philander opossum trapped in Para State, Northern Brazil. This study describes the complete full coding sequence and the genetic characterization of PIRYV. The genome sequence reveals that PIRYV has a typical vesiculovirus-like organization, encoding the five genes typical of the genus. Phylogenetic analysis confirmed that PIRYV is most closely related to Perinet virus and clustered in the same clade as Chandipura and Isfahan vesiculoviruses. PMID:27216928

  20. Genome Sequence of the Zoonotic Pathogen Chlamydophila psittaci▿

    PubMed Central

    Seth-Smith, Helena M. B.; Harris, Simon R.; Rance, Richard; West, Anthony P.; Severin, Juliette A.; Ossewaarde, Jacobus M.; Cutcliffe, Lesley T.; Skilton, Rachel J.; Marsh, Pete; Parkhill, Julian; Clarke, Ian N.; Thomson, Nicholas R.

    2011-01-01

    We present the first genome sequence of Chlamydophila psittaci, an intracellular pathogen of birds and a human zoonotic pathogen. A comparison with previously sequenced Chlamydophila genomes shows that, as in other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The C. psittaci plasmid was also sequenced. PMID:21183672

  1. Complete Genome Sequence of Mycobacterium abscessus subsp. bolletii

    PubMed Central

    Spilker, Theodore; LiPuma, John J.

    2016-01-01

    We report the complete genome sequence of a Mycobacterium abscessus subsp. bolletii isolate recovered from a sputum culture from an individual with cystic fibrosis. This sequence is the first completed whole-genome sequence of M. abscessus subsp. bolletii and adds value to studies of M. abscessus complex genomics. PMID:27284156

  2. Draft Genome Sequence of Rubrivivax gelatinosus CBS

    SciTech Connect

    Hu, P. S.; Lang, J.; Wawrousek, K.; Yu, J. P.; Maness, P. C.; Chen, J.

    2012-06-01

    Rubrivivax gelatinosus CBS, a purple nonsulfur photosynthetic bacterium, can grow photosynthetically using CO and N{sub 2} as the sole carbon and nitrogen nutrients, respectively. R. gelatinosus CBS is of particular interest due to its ability to metabolize CO and yield H{sub 2}. We present the 5-Mb draft genome sequence of R. gelatinosus CBS with the goal of providing genetic insight into the metabolic properties of this bacterium.

  3. Complete Genome Sequences of 138 Mycobacteriophages

    PubMed Central

    2012-01-01

    Bacteriophages are the most numerous biological entities in the biosphere, and although their genetic diversity is high, it remains ill defined. Mycobacteriophages—the viruses of mycobacterial hosts—provide insights into this diversity as well as tools for manipulating Mycobacterium tuberculosis. We report here the complete genome sequences of 138 new mycobacteriophages, which—together with the 83 mycobacteriophages previously reported—represent the largest collection of phages known to infect a single common host, Mycobacterium smegmatis mc2 155. PMID:22282335

  4. Complete genome sequence of Candidatus Ruthia magnifica.

    PubMed

    Roeselers, Guus; Newton, Irene L G; Woyke, Tanja; Auchtung, Thomas A; Dilly, Geoffrey F; Dutton, Rachel J; Fisher, Meredith C; Fontanez, Kristina M; Lau, Evan; Stewart, Frank J; Richardson, Paul M; Barry, Kerrie W; Saunders, Elizabeth; Detter, John C; Wu, Dongying; Eisen, Jonathan A; Cavanaugh, Colleen M

    2010-01-01

    The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis. PMID:21304746

  5. The predictive capacity of personal genome sequencing.

    PubMed

    Roberts, Nicholas J; Vogelstein, Joshua T; Parmigiani, Giovanni; Kinzler, Kenneth W; Vogelstein, Bert; Velculescu, Victor E

    2012-05-01

    New DNA sequencing methods will soon make it possible to identify all germline variants in any individual at a reasonable cost. However, the ability of whole-genome sequencing to predict predisposition to common diseases in the general population is unknown. To estimate this predictive capacity, we use the concept of a "genometype." A specific genometype represents the genomes in the population conferring a specific level of genetic risk for a specified disease. Using this concept, we estimated the maximum capacity of whole-genome sequencing to identify individuals at clinically significant risk for 24 different diseases. Our estimates were derived from the analysis of large numbers of monozygotic twin pairs; twins of a pair share the same genometype and therefore identical genetic risk factors. Our analyses indicate that (i) for 23 of the 24 diseases, most of the individuals will receive negative test results; (ii) these negative test results will, in general, not be very informative, because the risk of developing 19 of the 24 diseases in those who test negative will still be, at minimum, 50 to 80% of that in the general population; and (iii) on the positive side, in the best-case scenario, more than 90% of tested individuals might be alerted to a clinically significant predisposition to at least one disease. These results have important implications for the valuation of genetic testing by industry, health insurance companies, public policy-makers, and consumers. PMID:22472521

  6. Prenatal Diagnosis Innovation: Genome Sequencing of Maternal Plasma.

    PubMed

    Wong, Felix C K; Lo, Y M Dennis

    2016-01-01

    Noninvasive prenatal testing (NIPT) is accomplished by analysis of circulating cell-free fetal nucleic acids in maternal plasma. The advent of massively parallel sequencing (MPS) has enabled NIPT of chromosomal aneuploidies with unprecedented robustness, and these tests are now widely available for clinical use. Moreover, MPS-based NIPT of subchromosomal deletions/duplications and single-gene disorders has also been achieved, and the number of applications is growing. In addition to specific fetal genetic disorders, the whole fetal genome, transcriptome, and methylome have been revealed by deep sequencing of maternal plasma. The analysis of the fetal transcriptome and methylome may yield valuable information on fetal and maternal health. With continued improvement in sequencing technology and reduction in sequencing costs, the analysis of cell-free nucleic acids would play an increasingly important role in prenatal screening, diagnosis, monitoring, and risk stratification of fetal as well as maternal conditions. PMID:26473414

  7. Assessing the Costs and Cost-Effectiveness of Genomic Sequencing

    PubMed Central

    Christensen, Kurt D.; Dukhovny, Dmitry; Siebert, Uwe; Green, Robert C.

    2015-01-01

    Despite dramatic drops in DNA sequencing costs, concerns are great that the integration of genomic sequencing into clinical settings will drastically increase health care expenditures. This commentary presents an overview of what is known about the costs and cost-effectiveness of genomic sequencing. We discuss the cost of germline genomic sequencing, addressing factors that have facilitated the decrease in sequencing costs to date and anticipating the factors that will drive sequencing costs in the future. We then address the cost-effectiveness of diagnostic and pharmacogenomic applications of genomic sequencing, with an emphasis on the implications for secondary findings disclosure and the integration of genomic sequencing into general patient care. Throughout, we ground the discussion by describing efforts in the MedSeq Project, an ongoing randomized controlled clinical trial, to understand the costs and cost-effectiveness of integrating whole genome sequencing into cardiology and primary care settings. PMID:26690481

  8. Why Assembling Plant Genome Sequences Is So Challenging

    PubMed Central

    Claros, Manuel Gonzalo; Bautista, Rocío; Guerrero-Fernández, Darío; Benzerki, Hicham; Seoane, Pedro; Fernández-Pozo, Noé

    2012-01-01

    In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed. PMID:24832233

  9. Functional genomics of tomato in a post-genome-sequencing phase

    PubMed Central

    Aoki, Koh; Ogata, Yoshiyuki; Igarashi, Kaori; Yano, Kentaro; Nagasaki, Hideki; Kaminuma, Eli; Toyoda, Atsushi

    2013-01-01

    Completion of tomato genome sequencing project has broad impacts on genetic and genomic studies of tomato and Solanaceae plants. The reference genome sequence derived from Solanum lycopersicum cv ‘Heinz 1706’ serves as the firm basis for sequencing-based approaches to tomato genomics. In this article, we first present a brief summary of the genome sequencing project and a summary of the reference genome sequence. We then focus on recent progress in transcriptome sequencing and small RNA sequencing and show how the reference genome sequence makes these analyses more comprehensive than before. We discuss the potential of in-depth analysis that is based on DNA methylome sequencing and transcription start-site detection. Finally, we describe the current status of efforts to resequence S. lycopersicum cultivars to demonstrate how resequencing can allow the use of intraspecific genomic diversity for detailed phenotyping and breeding. PMID:23641177

  10. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

    PubMed Central

    Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca

    2015-01-01

    Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources. PMID:26151450

  11. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

    PubMed

    Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca

    2015-01-01

    Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources. PMID:26151450

  12. Whole Chloroplast Genome Sequencing in Fragaria Using Deep Sequencing: A Comparison of Three Methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chloroplast sequences previously investigated in Fragaria revealed low amounts of variation. Deep sequencing technologies enable economical sequencing of complete chloroplast genomes. These sequences can potentially provide robust phylogenetic resolution, even at low taxonomic levels within plant gr...

  13. Porcine parvovirus: DNA sequence and genome organization.

    PubMed

    Ranz, A I; Manclús, J J; Díaz-Aroca, E; Casal, J I

    1989-10-01

    We have determined the nucleotide sequence of an almost full-length clone of porcine parvovirus (PPV). The sequence is 4973 nucleotides (nt) long. The 3' end of virion DNA shows a Y-shaped configuration homologous to rodent parvoviruses. The 5' end of virion DNA shows a repetition of 127 nt at the carboxy terminus of the capsid proteins. The overall organization of the PPV genome is similar to those of other autonomous parvoviruses. There are two large open reading frames (ORFs) that almost entirely cover the genome, both located in the same frame of the complementary strand. The left ORF encodes the non-structural protein NS1 and the right ORF encodes the capsid proteins (VP1, VP2 and VP3). Promoter analysis, location of splicing sites and putative amino acid sequences for the viral proteins show a high homology of PPV with feline panleukopenia virus and canine parvoviruses (FPV and CPV) and rodent parvovirus. Therefore we conclude that PPV is related to the Kilham rat virus (KRV) group of autonomous parvoviruses formed by KRV, minute virus of mice, Lu III, H-1, FPV and CPV. PMID:2794971

  14. Simple sequence repeats in bryophyte mitochondrial genomes.

    PubMed

    Zhao, Chao-Xian; Zhu, Rui-Liang; Liu, Yang

    2016-01-01

    Simple sequence repeats (SSRs) are thought to be common in plant mitochondrial (mt) genomes, but have yet to be fully described for bryophytes. We screened the mt genomes of two liverworts (Marchantia polymorpha and Pleurozia purpurea), two mosses (Physcomitrella patens and Anomodon rugelii) and two hornworts (Phaeoceros laevis and Nothoceros aenigmaticus), and detected 475 SSRs. Some SSRs are found conserved during the evolution, among which except one exists in both liverworts and mosses, all others are shared only by the two liverworts, mosses or hornworts. SSRs are known as DNA tracts having high mutation rates; however, according to our observations, they still can evolve slowly. The conservativeness of these SSRs suggests that they are under strong selection and could play critical roles in maintaining the gene functions. PMID:24491104

  15. Initial sequencing and comparative analysis of the mouse genome

    SciTech Connect

    Waterston, Robert H.; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F.; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E.; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R.; Brown, Daniel G.; Brown, Stephen D.; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D.; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T.; Church, Deanna M.; Clamp, Michele; Clee, Christopher; Collins, Francis S.; Cook, Lisa L.; Copley, Richard R.; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D.; Deri, Justin; Dermitzakis, Emmanouil T.; Dewey, Colin; Dickens, Nicholas J.; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M.; Eddy, Sean R.; Elnitski, Laura; Emes, Richard D.; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A.; Flicek, Paul; Foley, Karen; Frankel, Wayne N.; Fulton, Lucinda A.; Fulton, Robert S.; Furey, Terrence S.; Gage, Diane; Gibbs, Richard A.; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A.; Green, Eric D.; Gregory, Simon; Guigo, Roderic; Guyer, Mark; Hardison, Ross C.; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W.; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B.; Johnson, L. Steven; Jones, Matthew; Jones, Thomas A.; Joy, Ann; Kamal, Michael; Karlsson, Elinor K.; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W. James; Kirby, Andrew; Kolbe, Diana L.; Korf, Ian; Kucherlapati, Raju S.; Kulbokas III, Edward J.; Kulp, David; Landers, Tom; Leger, J.P.; Leonard, Steven; Letunic, Ivica; Levine, Rosie; et al.

    2002-12-15

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  16. Draft Genome Sequence of Fungus Clonostachys rosea Strain YKD0085

    PubMed Central

    Liu, Shuai; Chang, Yaowen; Hu, Xujia; Gong, Xuanyun; Hao, Xiaojiang

    2016-01-01

    Here, we report the draft genome sequence of Clonostachys rosea (strain YKD0085). The functional annotation of C. rosea provides important information related to its ability to produce secondary metabolites. The genome sequence presented here builds the basis for further genome mining. PMID:27340057

  17. Complete Genome Sequence of Staphylococcus aureus Siphovirus Phage JS01

    PubMed Central

    Jia, Hongying; Bai, Qinqin; Yang, Yongchun

    2013-01-01

    Staphylococcus aureus is the most prevalent and economically significant pathogen causing bovine mastitis. We isolated and characterized one staphylophage from the milk of mastitis-affected cattle and sequenced its genome. Transmission electron microscopy (TEM) observation shows that it belongs to the family Siphovirus. We announce here its complete genome sequence and report major findings from the genomic analysis. PMID:24233583

  18. First Draft Genome Sequence of Staphylococcus condimenti F-2T

    PubMed Central

    Zheng, Beiwen; Hu, Xinjun; Jiang, Xiawei; Li, Ang; Yao, Jian

    2016-01-01

    This report describes the draft genome sequence of S. condimenti strain F-2T (DSM 11674), a potential starter culture. The genome assembly comprised 2,616,174 bp with 34.6% GC content. To the best of our knowledge, this is the first documentation that reports the whole-genome sequence of S. condimenti. PMID:27257207

  19. Draft Genome Sequence of Fungus Clonostachys rosea Strain YKD0085.

    PubMed

    Liu, Shuai; Chang, Yaowen; Hu, Xujia; Gong, Xuanyun; Di, Yingtong; Dong, Jinyan; Hao, Xiaojiang

    2016-01-01

    Here, we report the draft genome sequence of Clonostachys rosea (strain YKD0085). The functional annotation of C. rosea provides important information related to its ability to produce secondary metabolites. The genome sequence presented here builds the basis for further genome mining. PMID:27340057

  20. Draft Genome Sequence of the Fungus Trametes hirsuta 072

    PubMed Central

    Tyazhelova, Tatiana V.; Moiseenko, Konstantin V.; Vasina, Daria V.; Mosunova, Olga V.; Fedorova, Tatiana V.; Maloshenok, Lilya G.; Landesman, Elena O.; Bruskin, Sergei A.; Psurtseva, Nadezhda V.; Slesarev, Alexei I.; Kozyavkin, Sergei A.; Koroleva, Olga V.

    2015-01-01

    A standard draft genome sequence of the white rot saprotrophic fungus Trametes hirsuta 072 (Basidiomycota, Polyporales) is presented. The genome sequence contains about 33.6 Mb assembled in 141 scaffolds with a G+C content of ~57.6%. The draft genome annotation predicts 14,598 putative protein-coding open reading frames (ORFs). PMID:26586872

  1. Draft Genome Sequence of Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556.

    PubMed

    Komaki, Hisayuki; Ichikawa, Natsuko; Oguchi, Akio; Hamada, Moriyuki; Tamura, Tomohiko; Suzuki, Ken-Ichiro; Fujita, Nobuyuki

    2016-01-01

    Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces hygroscopicus subsp. hygroscopicus into the NBRC culture collection. An average nucleotide identity analysis confirmed that the taxonomic identification is correct. The genome sequence will serve as a valuable reference for genome mining to search new secondary metabolites. PMID:27198007

  2. Draft Genome Sequence of Alternaria alternata ATCC 34957.

    PubMed

    Nguyen, Hai D T; Lewis, Christopher T; Lévesque, C André; Gräfenhan, Tom

    2016-01-01

    We report the draft genome sequence of Alternaria alternata ATCC 34957. This strain was previously reported to produce alternariol and alternariol monomethyl ether on weathered grain sorghum. The genome was sequenced with PacBio technology and assembled into 27 scaffolds with a total genome size of 33.5 Mb. PMID:26769939

  3. First Draft Genome Sequence of Staphylococcus condimenti F-2T.

    PubMed

    Zheng, Beiwen; Hu, Xinjun; Jiang, Xiawei; Li, Ang; Yao, Jian; Li, Lanjuan

    2016-01-01

    This report describes the draft genome sequence of S. condimenti strain F-2(T) (DSM 11674), a potential starter culture. The genome assembly comprised 2,616,174 bp with 34.6% GC content. To the best of our knowledge, this is the first documentation that reports the whole-genome sequence of S. condimenti. PMID:27257207

  4. Whole-Genome Shotgun Sequencing of a Colonizing Multilocus Sequence Type 17 Streptococcus agalactiae Strain

    PubMed Central

    Singh, Pallavi; Springman, A. Cody; Davies, H. Dele

    2012-01-01

    This report highlights the whole-genome shotgun draft sequence for a Streptococcus agalactiae strain representing multilocus sequence type (ST) 17, isolated from a colonized woman at 8 weeks postpartum. This sequence represents an important addition to the published genomes and will promote comparative genomic studies of S. agalactiae recovered from diverse sources. PMID:23045509

  5. TAG Sequence Identification of Genomic Regions Using TAGdb.

    PubMed

    Ruperao, Pradeep

    2016-01-01

    Second-generation sequencing (SGS) technology has enabled the sequencing of genomes and identification of genes. However, large complex plant genomes remain particularly difficult for de novo assembly. Access to the vast quantity of raw sequence data may facilitate discoveries; however the volume of this data makes access difficult. This chapter discusses the Web-based tool TAGdb that enables researchers to identify paired read second-generation DNA sequence data that share identity with a submitted query sequence. The identified reads can be used for PCR amplification of genomic regions to identify genes and promoters without the need for genome assembly. PMID:26519409

  6. Genomic Sequence Comparisons, 1987-2003 Final Report

    SciTech Connect

    George M. Church

    2004-07-29

    This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed to one of the first complete DOE genome sequences, in 1997, that of Methanobacterium thermoautotropicum, a species of great relevance to energy-rich gas production.

  7. Complete genome sequence of Methanoculleus marisnigri type strain JR1

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Saunders, Elizabeth H; Han, Cliff; Brettin, Tom; Detter, J. Chris; Bruce, David; Mikhailova, Natalia; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.

  8. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  9. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    PubMed Central

    Anderson, Iain J.; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Pitluck, Sam; Hauser, Loren; Land, Miriam; Lucas, Susan; Richardson, Paul; Whitman, William B.; Kyrpides, Nikos C.

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal kingdom Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea. PMID:21304657

  10. Clinical genomics information management software linking cancer genome sequence and clinical decisions.

    PubMed

    Watt, Stuart; Jiao, Wei; Brown, Andrew M K; Petrocelli, Teresa; Tran, Ben; Zhang, Tong; McPherson, John D; Kamel-Reid, Suzanne; Bedard, Philippe L; Onetto, Nicole; Hudson, Thomas J; Dancey, Janet; Siu, Lillian L; Stein, Lincoln; Ferretti, Vincent

    2013-09-01

    Using sequencing information to guide clinical decision-making requires coordination of a diverse set of people and activities. In clinical genomics, the process typically includes sample acquisition, template preparation, genome data generation, analysis to identify and confirm variant alleles, interpretation of clinical significance, and reporting to clinicians. We describe a software application developed within a clinical genomics study, to support this entire process. The software application tracks patients, samples, genomic results, decisions and reports across the cohort, monitors progress and sends reminders, and works alongside an electronic data capture system for the trial's clinical and genomic data. It incorporates systems to read, store, analyze and consolidate sequencing results from multiple technologies, and provides a curated knowledge base of tumor mutation frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians. By supporting the entire process, the application provides deep support for clinical decision making, enabling the generation of relevant guidance in reports for verification by an expert panel prior to forwarding to the treating physician. PMID:23603536

  11. Mitochondrial genome sequencing in atherosclerosis: what's next?

    PubMed

    Sazonova, Margarita A; Shkurat, Tatiana P; Demakova, Natalya A; Zhelankin, Andrey V; Barinova, Valeria A; Sobenin, Igor A; Orekhov, Alexander N

    2016-01-01

    Cardiovascular diseases are currently a basic cause of mortality in highly developed countries. The major reason for genesis and development of cardiovascular diseases is atherosclerosis. At the present time high technology methods of molecular genetic diagnostics can significantly simplify early presymptomatic recognition of patients with atherosclerosis, to detect risk groups and to perform a family analysis of this pathology. A Next-Generation Sequencing (NGS) technology can be characterized by high productivity and cheapness of full genome analysis of each DNA sample. We suppose that in the nearest future NGS methods will be widely used for scientific and diagnostic purposes, including personalized medicine. In the present review article literature data on using NGS technology were described in studying mitochondrial genome mutations associated with atherosclerosis and its risk factors, such as mitochondrial diabetes, mitochondrial cardiomyopathy, diabetic nephropathy and left ventricular hypertrophy. With the use of the NGS technology it proved to be possible to detect a range of homoplasmic and heteroplasmic mutations and mitochondrial genome haplogroups which are associated with these pathologies. Meanwhile some mutations and haplogroups were detected both in atherosclerosis and in its risk factors. It conveys the suggestion that there are common pathogenetic mechanisms causing these pathologies. What comes next? New paradigm of crosstalk between non-pharmaceutical (including molecular genetic) and true pharmaceutical approaches may be developed to fill the niche of effective and pathogenically targeted pretreatment and treatment of preclinical and subclinical atherosclerosis to avoid the development of chronic life-threatening disease. PMID:26561059

  12. Detecting long tandem duplications in genomic sequences

    PubMed Central

    2012-01-01

    Background Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. Results In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,a we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS < 1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. Conclusions ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations. PMID:22568762

  13. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

    PubMed Central

    DiGuistini, Scott; Liao, Nancy Y; Platt, Darren; Robertson, Gordon; Seidel, Michael; Chan, Simon K; Docking, T Roderick; Birol, Inanc; Holt, Robert A; Hirst, Martin; Mardis, Elaine; Marra, Marco A; Hamelin, Richard C; Bohlmann, Jörg; Breuil, Colette; Jones, Steven JM

    2009-01-01

    Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data. PMID:19747388

  14. Complete Genome Sequence of Rift Valley Fever Virus Strain Lunyo

    PubMed Central

    Horton, Daniel L.; Marston, Denise A.; Johnson, Nicholas; Ellis, Richard J.; Fooks, Anthony R.; Hewson, Roger

    2016-01-01

    Using next-generation sequencing technologies, the first complete genome sequence of Rift Valley fever virus strain Lunyo is reported here. Originally reported as an attenuated antigenic variant strain from Uganda, genomic sequence analysis shows that Lunyo clusters together with other Ugandan isolates. PMID:27081121

  15. First Complete Genome Sequence of Cherry virus A

    PubMed Central

    Koinuma, Hiroaki; Nijo, Takamichi; Iwabuchi, Nozomu; Yoshida, Tetsuya; Keima, Takuya; Okano, Yukari; Maejima, Kensaku; Yamaji, Yasuyuki

    2016-01-01

    The 5′-terminal genomic sequence of Cherry virus A (CVA) has long been unknown. We determined the first complete genome sequence of an apricot isolate of CVA (7,434 nucleotides [nt]). The 5′-untranslated region was 107 nt in length, which was 53 nt longer than those of known CVA sequences. PMID:27284130

  16. Complete Genomic Sequence of Duck Flavivirus from China

    PubMed Central

    Liu, Ming; Liu, Chunguo; Li, Gang; Li, Xiaojun; Yin, Xiuchen; Chen, Yuhuan

    2012-01-01

    We report here the complete genomic sequence of the Chinese duck flavivirus TA strain. This work is the first to document the complete genomic sequence of this previously unknown duck flavivirus strain. The sequence will help further relevant epidemiological studies and extend our general knowledge of flaviviruses. PMID:22354941

  17. Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata

    PubMed Central

    Yamauchi, Kenta; Hamamoto, Makiko; Takahashi, Yurika; Ogura, Yoshitoshi; Hayashi, Tetsuya

    2015-01-01

    The draft genome sequence of the archiasomycetous yeast Saitoella complicata was determined. The assembly of newly and previously sequenced data sets resulted in 104 contigs (total of 14.1 Mbp; N50, 239 kbp). On the newly assembled genome, a total of 6,933 protein-coding sequences (7,119 transcripts, including alternative splicing forms) were identified. PMID:26021914

  18. First Complete Genome Sequence of Cherry virus A.

    PubMed

    Koinuma, Hiroaki; Nijo, Takamichi; Iwabuchi, Nozomu; Yoshida, Tetsuya; Keima, Takuya; Okano, Yukari; Maejima, Kensaku; Yamaji, Yasuyuki; Namba, Shigetou

    2016-01-01

    The 5'-terminal genomic sequence of Cherry virus A (CVA) has long been unknown. We determined the first complete genome sequence of an apricot isolate of CVA (7,434 nucleotides [nt]). The 5'-untranslated region was 107 nt in length, which was 53 nt longer than those of known CVA sequences. PMID:27284130

  19. Next Generation Sequencing at the University of Chicago Genomics Core

    SciTech Connect

    Faber, Pieter

    2013-04-24

    The University of Chicago Genomics Core provides University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation sequencing, Sanger sequencing / genotyping and micro-arrays (gene expression, genotyping, and methylation). The current presentation will highlight our capabilities in the area of ultra-high throughput sequencing analysis.

  20. Current challenges in de novo plant genome sequencing and assembly

    PubMed Central

    2012-01-01

    Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community. PMID:22546054

  1. Genome sequencing of the important oilseed crop Sesamum indicum L.

    PubMed

    Zhang, Haiyang; Miao, Hongmei; Wang, Lei; Qu, Lingbo; Liu, Hongyan; Wang, Qiang; Yue, Meiwang

    2013-01-01

    The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome. The status of this project and our planned analyses are described. PMID:23369264

  2. First complete genome sequence of infectious laryngotracheitis virus

    PubMed Central

    2011-01-01

    Background Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that causes acute respiratory disease in chickens worldwide. To date, only one complete genomic sequence of ILTV has been reported. This sequence was generated by concatenating partial sequences from six different ILTV strains. Thus, the full genomic sequence of a single (individual) strain of ILTV has not been determined previously. This study aimed to use high throughput sequencing technology to determine the complete genomic sequence of a live attenuated vaccine strain of ILTV. Results The complete genomic sequence of the Serva vaccine strain of ILTV was determined, annotated and compared to the concatenated ILTV reference sequence. The genome size of the Serva strain was 152,628 bp, with a G + C content of 48%. A total of 80 predicted open reading frames were identified. The Serva strain had 96.5% DNA sequence identity with the concatenated ILTV sequence. Notably, the concatenated ILTV sequence was found to lack four large regions of sequence, including 528 bp and 594 bp of sequence in the UL29 and UL36 genes, respectively, and two copies of a 1,563 bp sequence in the repeat regions. Considerable differences in the size of the predicted translation products of 4 other genes (UL54, UL30, UL37 and UL38) were also identified. More than 530 single-nucleotide polymorphisms (SNPs) were identified. Most SNPs were located within three genomic regions, corresponding to sequence from the SA-2 ILTV vaccine strain in the concatenated ILTV sequence. Conclusions This is the first complete genomic sequence of an individual ILTV strain. This sequence will facilitate future comparative genomic studies of ILTV by providing an appropriate reference sequence for the sequence analysis of other ILTV strains. PMID:21501528

  3. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)

    SciTech Connect

    Yasawong, Montri; Teshima, Hazuki; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Sikorski, Johannes; Pukall, Rudiger; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Draft Genome Sequences of Klebsiella variicola Plant Isolates

    PubMed Central

    Martínez-Romero, Esperanza; Silva-Sanchez, Jesús; Barrios, Humberto; Rodríguez-Medina, Nadia; Martínez-Barnetche, Jesús; Téllez-Sosa, Juan; Gómez-Barreto, Rosa Elena

    2015-01-01

    Three endophytic Klebsiella variicola isolates—T29A, 3, and 6A2, obtained from sugar cane stem, maize shoots, and banana leaves, respectively—were used for whole-genome sequencing. Here, we report the draft genome sequences of circular chromosomes and plasmids. The genomes contain plant colonization and cellulases genes. This study will help toward understanding the genomic basis of K. variicola interaction with plant hosts. PMID:26358599

  5. Draft Genome Sequences of Klebsiella variicola Plant Isolates.

    PubMed

    Martínez-Romero, Esperanza; Silva-Sanchez, Jesús; Barrios, Humberto; Rodríguez-Medina, Nadia; Martínez-Barnetche, Jesús; Téllez-Sosa, Juan; Gómez-Barreto, Rosa Elena; Garza-Ramos, Ulises

    2015-01-01

    Three endophytic Klebsiella variicola isolates-T29A, 3, and 6A2, obtained from sugar cane stem, maize shoots, and banana leaves, respectively-were used for whole-genome sequencing. Here, we report the draft genome sequences of circular chromosomes and plasmids. The genomes contain plant colonization and cellulases genes. This study will help toward understanding the genomic basis of K. variicola interaction with plant hosts. PMID:26358599

  6. Integration of new alternative reference strain genome sequences into the Saccharomyces genome database.

    PubMed

    Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla; Demeter, Janos; Engel, Stacia; Hellerstedt, Sage T; Karra, Kalpana; Hitz, Benjamin C; Nash, Robert S; Paskov, Kelley; Sheppard, Travis; Skrzypek, Marek; Weng, Shuai; Wong, Edith; Michael Cherry, J

    2016-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.Database URL: www.yeastgenome.org. PMID:27252399

  7. Integration of new alternative reference strain genome sequences into the Saccharomyces genome database

    PubMed Central

    Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C.; Dalusag, Kyla; Demeter, Janos; Engel, Stacia; Hellerstedt, Sage T.; Karra, Kalpana; Hitz, Benjamin C.; Nash, Robert S.; Paskov, Kelley; Sheppard, Travis; Skrzypek, Marek; Weng, Shuai; Wong, Edith; Michael Cherry, J.

    2016-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences. Database URL: www.yeastgenome.org PMID:27252399

  8. Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation.

    PubMed

    Hibsh, Dror; Buetow, Kenneth H; Yaari, Gur; Efroni, Sol

    2016-05-19

    The cancer genome is abnormal genome, and the ability to monitor its sequence had undergone a technological revolution. Yet prognosis and diagnosis remain an expert-based decision, with only limited abilities to provide machine-based decisions. We introduce a heterogeneity-based method for stratifying and visualizing whole-genome sequencing (WGS) reads. This method uses the heterogeneity within WGS reads to markedly reduce the dimensionality of next-generation sequencing data; it is available through the tool HiBS (Heterogeneity-Based Subclassification) that allows cancer sample classification. We validated HiBS using >200 WGS samples from nine different cancer types from The Cancer Genome Atlas (TCGA). With HiBS, we show progress with two WGS related issues: (i) differentiation between normal (NB) and tumor (TP) samples based solely on the information structure of their WGS data, and (ii) identification of specific regions of chromosomal amplification/deletion and their association with tumor stage. By comparing results to those obtained through available WGS analyses tools, we demonstrate some of the novelties obtained by the approach implemented in HiBS and also show nearly perfect normal/tumor classification, used to identify known and unknown chromosomal aberrations. Finally, the HiBS index has been associated with breast cancer tumor stage. PMID:26809676

  9. Genome sequencing and annotation of Proteus sp. SAS71

    PubMed Central

    Selim, Samy; Hassan, Sherif; Hagagy, Nashwa

    2015-01-01

    We report draft genome sequence of Proteus sp. strain SAS71, isolated from water spring in Aljouf region, Saudi Arabia. The draft genome size is 3,037,704 bp with a G + C content of 39.3% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA). The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDIU00000000. PMID:26697338

  10. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions fr...

  11. Sequencing and assembly of the 22-gb loblolly pine genome.

    PubMed

    Zimin, Aleksey; Stevens, Kristian A; Crepeau, Marc W; Holtz-Morris, Ann; Koriabine, Maxim; Marçais, Guillaume; Puiu, Daniela; Roberts, Michael; Wegrzyn, Jill L; de Jong, Pieter J; Neale, David B; Salzberg, Steven L; Yorke, James A; Langley, Charles H

    2014-03-01

    Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer "super-reads," rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp. PMID:24653210

  12. The reference genome sequence of Saccharomyces cerevisiae: then and now.

    PubMed

    Engel, Stacia R; Dietrich, Fred S; Fisk, Dianna G; Binkley, Gail; Balakrishnan, Rama; Costanzo, Maria C; Dwight, Selina S; Hitz, Benjamin C; Karra, Kalpana; Nash, Robert S; Weng, Shuai; Wong, Edith D; Lloyd, Paul; Skrzypek, Marek S; Miyasato, Stuart R; Simison, Matt; Cherry, J Michael

    2014-03-01

    The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science. PMID:24374639

  13. The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now

    PubMed Central

    Engel, Stacia R.; Dietrich, Fred S.; Fisk, Dianna G.; Binkley, Gail; Balakrishnan, Rama; Costanzo, Maria C.; Dwight, Selina S.; Hitz, Benjamin C.; Karra, Kalpana; Nash, Robert S.; Weng, Shuai; Wong, Edith D.; Lloyd, Paul; Skrzypek, Marek S.; Miyasato, Stuart R.; Simison, Matt; Cherry, J. Michael

    2014-01-01

    The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called “S288C 2010,” was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science. PMID:24374639

  14. Selection to sequence: opportunities in fungal genomics

    SciTech Connect

    Baker, Scott E.

    2009-12-01

    Selection is a biological force, causing genotypic and phenotypic change over time. Whether environmental or human induced, selective pressures shape the genotypes and the phenotypes of organisms both in nature and in the laboratory. In nature, selective pressure is highly dynamic and the sum of the environment and other organisms. In the laboratory, selection is used in genetic studies and industrial strain development programs to isolate mutants affecting biological processes of interest to researchers. Selective pressures are important considerations for fungal biology. In the laboratory a number of fungi are used as experimental systems to study a wide range of biological processes and in nature fungi are important pathogens of plants and animals and play key roles in carbon and nitrogen cycling. The continued development of high throughput sequencing technologies makes it possible to characterize at the genomic level, the effect of selective pressures both in the lab and in nature for filamentous fungi as well as other organisms.

  15. A taste of pineapple evolution through genome sequencing.

    PubMed

    Xu, Qing; Liu, Zhong-Jian

    2015-12-01

    The genome sequence assembly of the highly heterozygous Ananas comosus and its varieties is an impressive technical achievement. The sequence opens the door to a greater understanding of pineapple morphology and evolution. PMID:26620110

  16. Insights from twenty years of bacterial genome sequencing

    SciTech Connect

    Land, Miriam L; Hauser, Loren John; Jun, Se Ran; Nookaew, Intawat; Leuze, Michael Rex; Ahn, Tae-Hyuk; Karpinets, Tatiana V; Lund, Ole; Kora, Guruprasad H; Wassenaar, Trudy; Poudel, Suresh; Ussery, David W

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome

  17. Insights from 20 years of bacterial genome sequencing.

    PubMed

    Land, Miriam; Hauser, Loren; Jun, Se-Ran; Nookaew, Intawat; Leuze, Michael R; Ahn, Tae-Hyuk; Karpinets, Tatiana; Lund, Ole; Kora, Guruprased; Wassenaar, Trudy; Poudel, Suresh; Ussery, David W

    2015-03-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome

  18. Coevolution between simple sequence repeats (SSRs) and virus genome size

    PubMed Central

    2012-01-01

    Background Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes. Results In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome < 100 kb, genomes containing penta- and hexa- SSRs are not more than 50%. Principal components analysis (PCA) indicated that dinucleotide repeat affects the differences of SSRs most strongly among virus genomes. Results showed that SSRs tend to accumulate in larger virus genomes; and the longer genome sequence, the longer repeat units. Conclusions We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree. PMID:22931422

  19. Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64▿

    PubMed Central

    Shu, Hung-Wei; Liu, Tze-Tze; Chan, Huang-I; Liu, Yen-Ming; Wu, Keh-Ming; Shu, Hung-Yu; Tsai, Shih-Feng; Hsiao, Kwang-Jen; Hu, Wensi S.; Ng, Wailap Victor

    2011-01-01

    Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich M. fermentans strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain. PMID:21642450

  20. Whole-genome sequencing in outbreak analysis.

    PubMed

    Gilchrist, Carol A; Turner, Stephen D; Riley, Margaret F; Petri, William A; Hewlett, Erik L

    2015-07-01

    In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed. PMID:25876885

  1. Whole-Genome Sequencing in Outbreak Analysis

    PubMed Central

    Turner, Stephen D.; Riley, Margaret F.; Petri, William A.; Hewlett, Erik L.

    2015-01-01

    SUMMARY In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed. PMID:25876885

  2. Genome Project Standards in a New Era of Sequencing

    SciTech Connect

    GSC Consortia; HMP Jumpstart Consortia; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G.; Hostetler, J.; Muzny, D.; Detter, J. C.; Ali, J.; Birren, B.; Bruce, D. C.; Buhay, C.; Cole, J. R.; Ding, Y.; Dugan, S.; Field, D.; Garrity, G. M.; Gibbs, R.; Graves, T.; Han, C. S.; Harrison, S. H.; Highlander, S.; Hugenholtz, P.; Khouri, H. M.; Kodira, C. D.; Kolker, E.; Kyrpides, N. C.; Lang, D.; Lapidus, A.; Malfatti, S. A.; Markowitz, V.; Metha, T.; Nelson, K. E.; Parkhill, J.; Pitluck, S.; Qin, X.; Read, T. D.; Schmutz, J.; Sozhamannan, S.; Strausberg, R.; Sutton, G.; Thomson, N. R.; Tiedje, J. M.; Weinstock, G.; Wollam, A.

    2009-06-01

    For over a decade, genome 43 sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole genome sequencing that requires a careful reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker 'draft', however these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better reflect the

  3. Genome Wide Characterization of Simple Sequence Repeats in Cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The whole genome sequence of the cucumber cultivar Gy14 was recently sequenced at 15× coverage with the Roche 454 Titanium technology. The microsatellite DNA sequences (simple sequence repeats, SSRs) in the assembled scaffolds were computationally explored and characterized. A total of 112,073 SSRs ...

  4. Finishing The Euchromatic Sequence Of The Human Genome

    SciTech Connect

    Rubin, Edward M.; Lucas, Susan; Richardson, Paul; Rokhsar, Daniel; Pennacchio, Len

    2004-09-07

    The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process.The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers {approx}99% of the euchromatic genome and is accurate to an error rate of {approx}1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number,birth and death. Notably, the human genome seems to encode only20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.

  5. Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum

    PubMed Central

    Graupner, Katharina; Lackner, Gerald

    2015-01-01

    Janthinobacterium agaricidamnosum causes soft-rot disease of the cultured button mushroom Agaricus bisporus and is thus responsible for agricultural losses. Here, we present the genome sequence of J. agaricidamnosum DSM 9628. The 5.9-Mb genome harbors several secondary metabolite biosynthesis gene clusters, which renders this neglected bacterium a promising source for genome mining approaches. PMID:25883287

  6. Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum.

    PubMed

    Graupner, Katharina; Lackner, Gerald; Hertweck, Christian

    2015-01-01

    Janthinobacterium agaricidamnosum causes soft-rot disease of the cultured button mushroom Agaricus bisporus and is thus responsible for agricultural losses. Here, we present the genome sequence of J. agaricidamnosum DSM 9628. The 5.9-Mb genome harbors several secondary metabolite biosynthesis gene clusters, which renders this neglected bacterium a promising source for genome mining approaches. PMID:25883287

  7. SEQUENCING THE PIG GENOME USING A BAC BY BAC APPROACH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have generated a highly contiguous physical map covering >98% of the pig genome in just 176 contigs. The map is localized to the genome through integration with the UIVC RH map as well BAC end sequence alignments to the human genome. Over 265k HindIII restriction digest fingerprints totaling 16.2...

  8. First Complete Genome Sequence of a Subdivision 6 Acidobacterium Strain

    PubMed Central

    Vieira, Selma; Bunk, Boyke; Riedel, Thomas; Spröer, Cathrin; Overmann, Jörg

    2016-01-01

    Although ubiquitous and abundant in soils, acidobacteria have mostly escaped isolation and remain poorly investigated. Only a few cultured representatives and just eight genomes of subdivisions 1, 3, and 4 are available to date. Here, we determined the complete genome sequence of strain HEG_-6_39, the first genome of Acidobacterium subdivision 6. PMID:27231379

  9. Genome Sequence of Xanthomonas axonopodis pv. punicae Strain LMG 859

    PubMed Central

    Sharma, Vikas; Midha, Samriti; Ranjan, Manish; Pinnaka, Anil Kumar

    2012-01-01

    We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859, the causal agent of bacterial leaf blight disease in pomegranate. The draft genome will aid in comparative genomics, epidemiological studies, and quarantine of this devastating phytopathogen. PMID:22493202

  10. Draft Genome Sequence of a Diarrheagenic Morganella morganii Isolate

    PubMed Central

    Singh, Pallavi; Mosci, Rebekah; Rudrik, James T.

    2015-01-01

    This is a report of the whole-genome draft sequence of a diarrheagenic Morganella morganii isolate from a patient in Michigan, USA. This genome represents an important addition to the limited number of pathogenic M. morganii genomes available. PMID:26450735

  11. Genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859.

    PubMed

    Sharma, Vikas; Midha, Samriti; Ranjan, Manish; Pinnaka, Anil Kumar; Patil, Prabhu B

    2012-05-01

    We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859, the causal agent of bacterial leaf blight disease in pomegranate. The draft genome will aid in comparative genomics, epidemiological studies, and quarantine of this devastating phytopathogen. PMID:22493202

  12. Draft Genome Sequence of Neurospora crassa Strain FGSC 73

    SciTech Connect

    Baker, Scott E.; Schackwitz, Wendy; Lipzen, Anna; Martin, Joel; Haridas, Sajeet; LaButti, Kurt; Grigoriev, Igor V.; Simmons, Blake A.; McCluskey, Kevin

    2015-04-02

    We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a, trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models.

  13. Complete Genome Sequence of Bacillus megaterium Bacteriophage Eldridge

    PubMed Central

    Reveille, Alexandra M.; Eldridge, Kimberly A.

    2016-01-01

    In this study the complete genome sequence of the unique bacteriophage Eldridge, isolated from soil using Bacillus megaterium as the host organism, was determined. Eldridge is a myovirus with a genome consisting of 242 genes and is unique when compared to phage sequences in GenBank. PMID:27103735

  14. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis.

    PubMed

    Eppinger, Mark; McNair, Katelyn; Zogaj, Xhavit; Dinsdale, Elizabeth A; Edwards, Robert A; Klose, Karl E

    2013-01-01

    Piscirickettsia salmonis is a Gram-negative intracellular fish pathogen that has a significant impact on the salmon industry. Here, we report the genome sequence of P. salmonis strain LF-89. This is the first draft genome sequence of P. salmonis, and it reveals interesting attributes, including flagellar genes, despite this bacterium being considered nonmotile. PMID:24201203

  15. Complete Genome Sequences of Five Paenibacillus larvae Bacteriophages.

    PubMed

    Sheflo, Michael A; Gardner, Adam V; Merrill, Bryan D; Fisher, Joshua N B; Lunt, Bryce L; Breakwell, Donald P; Grose, Julianne H; Burnett, Sandra H

    2013-01-01

    Paenibacillus larvae is a pathogen of honeybees that causes American foulbrood (AFB). We isolated bacteriophages from soil containing bee debris collected near beehives in Utah. We announce five high-quality complete genome sequences, which represent the first completed genome sequences submitted to GenBank for any P. larvae bacteriophage. PMID:24233582

  16. Initial sequencing and analysis of the human genome.

    PubMed

    Lander, E S; Linton, L M; Birren, B; Nusbaum, C; Zody, M C; Baldwin, J; Devon, K; Dewar, K; Doyle, M; FitzHugh, W; Funke, R; Gage, D; Harris, K; Heaford, A; Howland, J; Kann, L; Lehoczky, J; LeVine, R; McEwan, P; McKernan, K; Meldrim, J; Mesirov, J P; Miranda, C; Morris, W; Naylor, J; Raymond, C; Rosetti, M; Santos, R; Sheridan, A; Sougnez, C; Stange-Thomann, Y; Stojanovic, N; Subramanian, A; Wyman, D; Rogers, J; Sulston, J; Ainscough, R; Beck, S; Bentley, D; Burton, J; Clee, C; Carter, N; Coulson, A; Deadman, R; Deloukas, P; Dunham, A; Dunham, I; Durbin, R; French, L; Grafham, D; Gregory, S; Hubbard, T; Humphray, S; Hunt, A; Jones, M; Lloyd, C; McMurray, A; Matthews, L; Mercer, S; Milne, S; Mullikin, J C; Mungall, A; Plumb, R; Ross, M; Shownkeen, R; Sims, S; Waterston, R H; Wilson, R K; Hillier, L W; McPherson, J D; Marra, M A; Mardis, E R; Fulton, L A; Chinwalla, A T; Pepin, K H; Gish, W R; Chissoe, S L; Wendl, M C; Delehaunty, K D; Miner, T L; Delehaunty, A; Kramer, J B; Cook, L L; Fulton, R S; Johnson, D L; Minx, P J; Clifton, S W; Hawkins, T; Branscomb, E; Predki, P; Richardson, P; Wenning, S; Slezak, T; Doggett, N; Cheng, J F; Olsen, A; Lucas, S; Elkin, C; Uberbacher, E; Frazier, M; Gibbs, R A; Muzny, D M; Scherer, S E; Bouck, J B; Sodergren, E J; Worley, K C; Rives, C M; Gorrell, J H; Metzker, M L; Naylor, S L; Kucherlapati, R S; Nelson, D L; Weinstock, G M; Sakaki, Y; Fujiyama, A; Hattori, M; Yada, T; Toyoda, A; Itoh, T; Kawagoe, C; Watanabe, H; Totoki, Y; Taylor, T; Weissenbach, J; Heilig, R; Saurin, W; Artiguenave, F; Brottier, P; Bruls, T; Pelletier, E; Robert, C; Wincker, P; Smith, D R; Doucette-Stamm, L; Rubenfield, M; Weinstock, K; Lee, H M; Dubois, J; Rosenthal, A; Platzer, M; Nyakatura, G; Taudien, S; Rump, A; Yang, H; Yu, J; Wang, J; Huang, G; Gu, J; Hood, L; Rowen, L; Madan, A; Qin, S; Davis, R W; Federspiel, N A; Abola, A P; Proctor, M J; Myers, R M; Schmutz, J; Dickson, M; Grimwood, J; Cox, D R; Olson, M V; Kaul, R; Raymond, C; Shimizu, N; Kawasaki, K; Minoshima, S; Evans, G A; Athanasiou, M; Schultz, R; Roe, B A; Chen, F; Pan, H; Ramser, J; Lehrach, H; Reinhardt, R; McCombie, W R; de la Bastide, M; Dedhia, N; Blöcker, H; Hornischer, K; Nordsiek, G; Agarwala, R; Aravind, L; Bailey, J A; Bateman, A; Batzoglou, S; Birney, E; Bork, P; Brown, D G; Burge, C B; Cerutti, L; Chen, H C; Church, D; Clamp, M; Copley, R R; Doerks, T; Eddy, S R; Eichler, E E; Furey, T S; Galagan, J; Gilbert, J G; Harmon, C; Hayashizaki, Y; Haussler, D; Hermjakob, H; Hokamp, K; Jang, W; Johnson, L S; Jones, T A; Kasif, S; Kaspryzk, A; Kennedy, S; Kent, W J; Kitts, P; Koonin, E V; Korf, I; Kulp, D; Lancet, D; Lowe, T M; McLysaght, A; Mikkelsen, T; Moran, J V; Mulder, N; Pollara, V J; Ponting, C P; Schuler, G; Schultz, J; Slater, G; Smit, A F; Stupka, E; Szustakowki, J; Thierry-Mieg, D; Thierry-Mieg, J; Wagner, L; Wallis, J; Wheeler, R; Williams, A; Wolf, Y I; Wolfe, K H; Yang, S P; Yeh, R F; Collins, F; Guyer, M S; Peterson, J; Felsenfeld, A; Wetterstrand, K A; Patrinos, A; Morgan, M J; de Jong, P; Catanese, J J; Osoegawa, K; Shizuya, H; Choi, S; Chen, Y J; Szustakowki, J

    2001-02-15

    The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence. PMID:11237011

  17. Complete genome sequence of ‘Candidatus Liberibacter africanus’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genome sequence of ‘Candidatus Liberibacter africanus’ (Laf), strain ptsapsy, was obtained by an Illumina HiSeq 2000. The Laf genome comprises 1,192,232 nucleotides, 34.5% GC content, 1,141 predicted coding sequences, 44 tRNAs, 3 complete copies of ribosomal RNA genes (16S, 23S and 5S) ...

  18. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis

    PubMed Central

    Eppinger, Mark; McNair, Katelyn; Zogaj, Xhavit; Dinsdale, Elizabeth A.; Edwards, Robert A.

    2013-01-01

    Piscirickettsia salmonis is a Gram-negative intracellular fish pathogen that has a significant impact on the salmon industry. Here, we report the genome sequence of P. salmonis strain LF-89. This is the first draft genome sequence of P. salmonis, and it reveals interesting attributes, including flagellar genes, despite this bacterium being considered nonmotile. PMID:24201203

  19. Selection of sequence variants to improve dairy cattle genomic predictions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic prediction reliabilities improved when adding selected sequence variants from run 5 of the 1,000 bull genomes project. High density (HD) imputed genotypes for 26,970 progeny tested Holstein bulls were combined with sequence variants for 444 Holstein animals. The first test included 481,904 c...

  20. The carrot genome sequence brings colors out of the dark.

    PubMed

    Garcia-Mas, Jordi; Rodriguez-Concepcion, Manuel

    2016-05-27

    The genome sequence of carrot (Daucus carota L.) is the first completed for an Apiaceae species, furthering knowledge of the evolution of the important euasterid II clade. Analyzing the whole-genome sequence allowed for the identification of a gene that may regulate the accumulation of carotenoids in the root. PMID:27230684

  1. Draft Genome Sequence of “Cohnella kolymensis” B-2846

    PubMed Central

    Kudryashova, Ekaterina B.; Ariskina, Elena V.

    2016-01-01

    A draft genome sequence of “Cohnella kolymensis” strain B-2846 was derived using IonTorrent sequencing technology. The size of the assembly and G+C content were in agreement with those of other species of this genus. Characterization of the genome of a novel species of Cohnella will assist in bacterial systematics. PMID:26769947

  2. Complete Genome Sequence of Enterococcus faecium ATCC 700221.

    PubMed

    McKenney, Peter T; Ling, Lilan; Wang, Guilin; Mane, Shrikant; Pamer, Eric G

    2016-01-01

    We report the complete genome sequence of a vancomycin-resistant isolate of Enterococcus faecium derived from human feces. The genome comprises one chromosome of 2.9 Mb and three plasmids. The strain harbors a plasmid-borne vanA-type vancomycin resistance locus and is a member of multilocus sequencing type (MLST) cluster ST-17. PMID:27198022

  3. Full Genome Sequence of a Bovine Enterovirus Isolated in China

    PubMed Central

    Peng, Xiao-wei; Dong, Hao; Wu, Qing-min

    2014-01-01

    We report the full genome sequence of an isolate of bovine enterovirus type B from China. The virus (BEV-BJ001) was isolated from Beijing, China, from fecal swabs of cattle suffering from severe diarrhea. This genome sequence will give useful insight for future molecular epidemiological studies in China. PMID:24970832

  4. Complete Genome Sequence of a Clinical Isolate of Enterobacter asburiae

    PubMed Central

    Liu, Feng; Yang, Jian; Xiao, Yan; Li, Li; Jin, Qi

    2016-01-01

    We report here the complete genome sequence of Enterobacter asburiae strain ENIPBJ-CG1, isolated from a bone marrow transplant patient. The size of the genome sequence is approximately 4.65 Mb, with a G+C content of 55.76%, and it is predicted to contain 4,790 protein-coding genes. PMID:27284137

  5. Almost finished: the complete genome sequence of Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mycosphaerella graminicola causes septoria tritici blotch of wheat. An 8.9x shotgun sequence of bread wheat strain IPO323 was generated through the Community Sequencing Program of the U.S. Department of Energy’s Joint Genome Institute (JGI), and was finished at the Stanford Human Genome Center. The ...

  6. Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877

    PubMed Central

    Bayjanov, Jumamurat R.; Joncour, Pauline; Hughes, Sandrine; Gillet, Benjamin; Kleerebezem, Michiel; Siezen, Roland; van Hijum, Sacha A. F. T.

    2015-01-01

    Lactobacillus plantarum is a versatile bacterial species that is isolated mostly from foods. Here, we present the first genome sequence of L. plantarum strain NIZO2877 isolated from a hot dog in Vietnam. Its two contigs represent a nearly complete genome sequence. PMID:26607887

  7. On the current status of Phakopsora pachyrhizi genome sequencing

    PubMed Central

    Loehrer, Marco; Vogel, Alexander; Huettel, Bruno; Reinhardt, Richard; Benes, Vladimir; Duplessis, Sébastien; Usadel, Björn; Schaffrath, Ulrich

    2014-01-01

    Recent advances in the field of sequencing technologies and bioinformatics allow a more rapid access to genomes of non-model organisms at sinking costs. Accordingly, draft genomes of several economically important cereal rust fungi have been released in the last 3 years. Aside from the very recent flax rust and poplar rust draft assemblies there are no genomic data available for other dicot-infecting rust fungi. In this article we outline rust fungus sequencing efforts and comment on the current status of Phakopsora pachyrhizi (Asian soybean rust) genome sequencing. PMID:25221558

  8. On the current status of Phakopsora pachyrhizi genome sequencing.

    PubMed

    Loehrer, Marco; Vogel, Alexander; Huettel, Bruno; Reinhardt, Richard; Benes, Vladimir; Duplessis, Sébastien; Usadel, Björn; Schaffrath, Ulrich

    2014-01-01

    Recent advances in the field of sequencing technologies and bioinformatics allow a more rapid access to genomes of non-model organisms at sinking costs. Accordingly, draft genomes of several economically important cereal rust fungi have been released in the last 3 years. Aside from the very recent flax rust and poplar rust draft assemblies there are no genomic data available for other dicot-infecting rust fungi. In this article we outline rust fungus sequencing efforts and comment on the current status of Phakopsora pachyrhizi (Asian soybean rust) genome sequencing. PMID:25221558

  9. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.

    PubMed

    Binnewies, Tim T; Motro, Yair; Hallin, Peter F; Lund, Ole; Dunn, David; La, Tom; Hampson, David J; Bellgard, Matthew; Wassenaar, Trudy M; Ussery, David W

    2006-07-01

    It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: "What have we learned from this vast amount of new genomic data?" Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity--even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this

  10. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements.

    PubMed

    Bull, Matthew J; Marchesi, Julian R; Vandamme, Peter; Plummer, Sue; Mahenthiralingam, Eshwar

    2012-04-01

    Multiple bioinformatic methods are available to analyse the information encoded within the complete genome sequence of a bacterium and accurately assign its species status or nearest phylogenetic neighbour. However, it is clear that even now in what is the third decade of bacterial genomics, taxonomically incorrect genome sequence depositions are still being made. We outline a simple scheme of bioinformatic analysis and a set of minimum criteria that should be applied to all bacterial genomic data to ensure that they are accurately assigned to the species or genus level prior to database deposition. To illustrate the utility of the bioinformatic workflow, we analysed the recently deposited genome sequence of Lactobacillus acidophilus 30SC and demonstrated that this DNA was in fact derived from a strain of Lactobacillus amylovorus. Using these methods researchers can ensure that the taxonomic accuracy of genome sequence depositions is maintained within the ever increasing nucleic acid datasets. PMID:22366464

  11. From complete genome sequence to “complete“ understanding?

    PubMed Central

    Galperin, Michael Y.; Koonin, Eugene V.

    2011-01-01

    The rapidly accumulating genome sequence data allow researchers to address fundamental biological questions that were not even asked just a few years ago. A major problem in genomics is the widening gap between the rapid progress in genome sequencing and the comparatively slow progress in the functional characterization of sequenced genomes. Here we discuss two key questions of genome biology: whether we need more genomes, and how deep is our understanding of biology based on genomic analysis. We argue that overly specific annotations of gene functions are often less useful than the more generic, but also more robust, functional assignments based on protein family classification. We also discuss problems in understanding the functions of the remaining “conserved hypothetical” genes. PMID:20647113

  12. Live genomics for pathogen monitoring in public health.

    PubMed

    D'Auria, Giuseppe; Schneider, Maria Victoria; Moya, Andrés

    2014-01-01

    Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the "local" level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a "streaming approach" (pipeline). Such pipeline would NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted "comprehensible" results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences. PMID:25437609

  13. Live Genomics for Pathogen Monitoring in Public Health

    PubMed Central

    D’Auria, Giuseppe; Schneider, Maria Victoria; Moya, Andrés

    2014-01-01

    Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in a short lapse of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the “local” level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a “streaming approach” (pipeline). Such pipeline would include NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted “comprehensible” results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences. PMID:25437609

  14. De novo assembly of a bell pepper endornavirus genome sequence using RNA sequencing data.

    PubMed

    Jo, Yeonhwa; Choi, Hoseng; Cho, Won Kyong

    2015-01-01

    The genus Endornavirus is a double-stranded RNA virus that infects a wide range of hosts. In this study, we report on the de novo assembly of a bell pepper endornavirus genome sequence by RNA sequencing (RNA-Seq). Our result demonstrates the successful application of RNA-Seq to obtain a complete viral genome sequence from the transcriptome data. PMID:25792042

  15. Genome sequencing and annotation of Serratia sp. strain TEL.

    PubMed

    Lephoto, Tiisetso E; Gray, Vincent M

    2015-12-01

    We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000. PMID:26697332

  16. Computational Profiling of Microbial Genomes using Short Sequences

    NASA Astrophysics Data System (ADS)

    Doering, Dale; Tsukuda, Toyoko

    2001-03-01

    The genomes of a number of microbial species have now been completely sequenced. We have developed a program for the statistical analysis of the appearance frequency and location of short DNA segments within an entire microbial genome. Using this program, the genomes of Methanococcus jannischii (1.66 Mbase; 68radiodurans (3.28 Mbase; 66and compared to a randomly generated genomic pattern. The random sequence shows the expected statistical frequency distribution about the average that equals the genome size divided by the total number of N size short segments (4N). In contrast, the microbial genomes are radically skewed with a large number of segments that rarely occur and a few that are highly represented in the genome. The specific distribution profile of the segments is strongly dependent on the overall bias in the organism. The biased appearance frequency allows us to develop a genome signature of each microbial species.

  17. Microbial genome sequencing using optical mapping and Illumina sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction Optical mapping is a technique in which strands of genomic DNA are digested with one or more restriction enzymes, and a physical map of the genome constructed from the resulting image. In outline, genomic DNA is extracted from a pure culture, linearly arrayed on a specialized glass sli...

  18. Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi

    SciTech Connect

    Schutzer S. E.; Dunn J.; Fraser-Liggett, C. M.; Casjens, S. R.; Qiu, W.-G.; Mongodin, E. F.; Luft, B. J.

    2011-02-01

    Borrelia burgdorferi is a causative agent of Lyme disease in North America and Eurasia. The first complete genome sequence of B. burgdorferi strain 31, available for more than a decade, has assisted research on the pathogenesis of Lyme disease. Because a single genome sequence is not sufficient to understand the relationship between genotypic and geographic variation and disease phenotype, we determined the whole-genome sequences of 13 additional B. burgdorferi isolates that span the range of natural variation. These sequences should allow improved understanding of pathogenesis and provide a foundation for novel detection, diagnosis, and prevention strategies.

  19. Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14.

    PubMed

    Stahl, Buffy; Barrangou, Rodolphe

    2013-01-01

    We present the 1,991,830-bp complete genome sequence of Lactobacillus acidophilus strain La-14 (SD-5212). Comparative genomic analysis revealed 99.98% similarity overall to the L. acidophilus NCFM genome. Globally, 111 single nucleotide polymorphisms (SNPs) (95 SNPs, 16 indels) were observed throughout the genome. Also, a 416-bp deletion in the LA14_1146 sugar ABC transporter was identified. PMID:23788546

  20. 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...

  1. MIPS: a database for genomes and protein sequences

    PubMed Central

    Mewes, H. W.; Frishman, D.; Gruber, C.; Geier, B.; Haase, D.; Kaps, A.; Lemcke, K.; Mannhaupt, G.; Pfeiffer, F.; Schüller, C.; Stocker, S.; Weil, B.

    2000-01-01

    The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried, near Munich, Germany, continues its longstanding tradition to develop and maintain high quality curated genome databases. In addition, efforts have been intensified to cover the wealth of complete genome sequences in a systematic, comprehensive form. Bioinformatics, supporting national as well as European sequencing and functional analysis projects, has resulted in several up-to-date genome-oriented databases. This report describes growing databases reflecting the progress of sequencing the Arabidopsis thaliana (MATDB) and Neurospora crassa genomes (MNCDB), the yeast genome database (MYGD) extended by functional analysis data, the database of annotated human EST-clusters (HIB) and the database of the complete cDNA sequences from the DHGP (German Human Genome Project). It also contains information on the up-to-date database of complete genomes (PEDANT), the classification of protein sequences (ProtFam) and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database. These databases can be accessed through the MIPS WWW server (http://www. mips.biochem.mpg.de ). PMID:10592176

  2. The diploid genome sequence of an Asian individual

    PubMed Central

    Wang, Jun; Wang, Wei; Li, Ruiqiang; Li, Yingrui; Tian, Geng; Goodman, Laurie; Fan, Wei; Zhang, Junqing; Li, Jun; Zhang, Juanbin; Guo, Yiran; Feng, Binxiao; Li, Heng; Lu, Yao; Fang, Xiaodong; Liang, Huiqing; Du, Zhenglin; Li, Dong; Zhao, Yiqing; Hu, Yujie; Yang, Zhenzhen; Zheng, Hancheng; Hellmann, Ines; Inouye, Michael; Pool, John; Yi, Xin; Zhao, Jing; Duan, Jinjie; Zhou, Yan; Qin, Junjie; Ma, Lijia; Li, Guoqing; Yang, Zhentao; Zhang, Guojie; Yang, Bin; Yu, Chang; Liang, Fang; Li, Wenjie; Li, Shaochuan; Li, Dawei; Ni, Peixiang; Ruan, Jue; Li, Qibin; Zhu, Hongmei; Liu, Dongyuan; Lu, Zhike; Li, Ning; Guo, Guangwu; Zhang, Jianguo; Ye, Jia; Fang, Lin; Hao, Qin; Chen, Quan; Liang, Yu; Su, Yeyang; san, A.; Ping, Cuo; Yang, Shuang; Chen, Fang; Li, Li; Zhou, Ke; Zheng, Hongkun; Ren, Yuanyuan; Yang, Ling; Gao, Yang; Yang, Guohua; Li, Zhuo; Feng, Xiaoli; Kristiansen, Karsten; Wong, Gane Ka-Shu; Nielsen, Rasmus; Durbin, Richard; Bolund, Lars; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian

    2009-01-01

    Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics. PMID:18987735

  3. Sequencing genomes from single cells by polymerase cloning.

    PubMed

    Zhang, Kun; Martiny, Adam C; Reppas, Nikos B; Barry, Kerrie W; Malek, Joel; Chisholm, Sallie W; Church, George M

    2006-06-01

    Genome sequencing currently requires DNA from pools of numerous nearly identical cells (clones), leaving the genome sequences of many difficult-to-culture microorganisms unattainable. We report a sequencing strategy that eliminates culturing of microorganisms by using real-time isothermal amplification to form polymerase clones (plones) from the DNA of single cells. Two Escherichia coli plones, analyzed by Affymetrix chip hybridization, demonstrate that plonal amplification is specific and the bias is randomly distributed. Whole-genome shotgun sequencing of Prochlorococcus MIT9312 plones showed 62% coverage of the genome from one plone at a sequencing depth of 3.5x, and 66% coverage from a second plone at a depth of 4.7x. Genomic regions not revealed in the initial round of sequencing are recovered by sequencing PCR amplicons derived from plonal DNA. The mutation rate in single-cell amplification is <2 x 10(5), better than that of current genome sequencing standards. Polymerase cloning should provide a critical tool for systematic characterization of genome diversity in the biosphere. PMID:16732271

  4. Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

    SciTech Connect

    McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

    2005-08-26

    Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

  5. Genome Sequence of the Trichosporon asahii Environmental Strain CBS 8904

    PubMed Central

    Li, Hai Tao; Zhu, He; Zhou, Guang Peng; Wang, Meng; Wang, Lei

    2012-01-01

    This is the first report of the genome sequence of Trichosporon asahii environmental strain CBS 8904, which was isolated from maize cobs. Comparison of the genome sequence with that of clinical strain CBS 2479 revealed that they have >99% chromosomal and mitochondrial sequence identity, yet CBS 8904 has 368 specific genes. Analysis of clusters of orthologous groups predicted that 3,307 genes belong to 23 functional categories and 703 genes were predicted to have a general function. PMID:23193141

  6. Whole-exome targeted sequencing of the uncharacterized pine genome.

    PubMed

    Neves, Leandro G; Davis, John M; Barbazuk, William B; Kirst, Matias

    2013-07-01

    The large genome size of many species hinders the development and application of genomic tools to study them. For instance, loblolly pine (Pinus taeda L.), an ecologically and economically important conifer, has a large and yet uncharacterized genome of 21.7 Gbp. To characterize the pine genome, we performed exome capture and sequencing of 14 729 genes derived from an assembly of expressed sequence tags. Efficiency of sequence capture was evaluated and shown to be similar across samples with increasing levels of complexity, including haploid cDNA, haploid genomic DNA and diploid genomic DNA. However, this efficiency was severely reduced for probes that overlapped multiple exons, presumably because intron sequences hindered probe:exon hybridizations. Such regions could not be entirely avoided during probe design, because of the lack of a reference sequence. To improve the throughput and reduce the cost of sequence capture, a method to multiplex the analysis of up to eight samples was developed. Sequence data showed that multiplexed capture was reproducible among 24 haploid samples, and can be applied for high-throughput analysis of targeted genes in large populations. Captured sequences were de novo assembled, resulting in 11 396 expanded and annotated gene models, significantly improving the knowledge about the pine gene space. Interspecific capture was also evaluated with over 98% of all probes designed from P. taeda that were efficient in sequence capture, were also suitable for analysis of the related species Pinus elliottii Engelm. PMID:23551702

  7. Using BLAT to find sequence similarity in closely related genomes.

    PubMed

    Bhagwat, Medha; Young, Lynn; Robison, Rex R

    2012-03-01

    The BLAST-Like Alignment Tool (BLAT) is used to find genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole-genome random reads to the human genome at a higher speed. It is freely available either on the Web or as a downloadable stand-alone program. BLAT search results provide a link for visualization in the University of California, Santa Cruz (UCSC) Genome Browser, where associated biological information may be obtained. Three example protocols are given: using an mRNA sequence to identify the exon-intron locations and associated gene in the genomic sequence of the same species, using a protein sequence to identify the coding regions in a genomic sequence and to search for gene family members in the same species, and using a protein sequence to find homologs in another species. PMID:22389010

  8. Savant: genome browser for high-throughput sequencing data

    PubMed Central

    Fiume, Marc; Williams, Vanessa; Brook, Andrew; Brudno, Michael

    2010-01-01

    Motivation: The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictions and understand the functional effects, especially in the context of other datasets. Results: We introduce Savant, the Sequence Annotation, Visualization and ANalysis Tool, a desktop visualization and analysis browser for genomic data. Savant was developed for visualizing and analyzing HTS data, with special care taken to enable dynamic visualization in the presence of gigabases of genomic reads and references the size of the human genome. Savant supports the visualization of genome-based sequence, point, interval and continuous datasets, and multiple visualization modes that enable easy identification of genomic variants (including single nucleotide polymorphisms, structural and copy number variants), and functional genomic information (e.g. peaks in ChIP-seq data) in the context of genomic annotations. Availability: Savant is freely available at http://compbio.cs.toronto.edu/savant Contact: savant@cs.toronto.edu PMID:20562449

  9. Reference genome sequence of the model plant Setaria

    SciTech Connect

    Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C.; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chuyu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela; Panaud, Olivier; Kellogg, Elizabeth A.; Brutnell, Thomas P.; Doust, Andrew N.; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  10. Reference genome sequence of the model plant Setaria

    SciTech Connect

    Bennetzen, Jeffrey L; Yang, Xiaohan; Ye, Chuyu; Tuskan, Gerald A

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The {approx}400-Mb assembly covers {approx}80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  11. Genome Science: A Video Tour of the Washington University Genome Sequencing Center for High School and Undergraduate Students

    ERIC Educational Resources Information Center

    Flowers, Susan K.; Easter, Carla; Holmes, Andrea; Cohen, Brian; Bednarski, April E.; Mardis, Elaine R.; Wilson, Richard K.; Elgin, Sarah C. R.

    2005-01-01

    Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other genomes. In 2004, a partnership was formed between Washington University School of Medicine Genome Sequencing Center's Outreach Program and Washington…

  12. Marsupial genome sequences: providing insight into evolution and disease.

    PubMed

    Deakin, Janine E

    2012-01-01

    Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences. PMID:24278712

  13. An international plan to sequence the nuclear genome of onion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As large-scale DNA sequencing technologies become more efficient and less costly, the genomic DNAs of more and more plants are being sequenced, assembled, and annotated. These complete sequences are extremely valuable for the identification of specific genes associated with important phenotypes. Thi...

  14. Genome sequencing of the redbanded stink bug (Piezodorus guildinii)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We assembled a partial genome sequence from the redbanded stink bug, Piezodorus guildinii from Illumina MiSeq sequencing runs. The sequence has been submitted and published under NCBI GenBank Accession Number JTEQ01000000. The BioProject and BioSample Accession numbers are PRJNA263369 and SAMN030997...

  15. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)

    SciTech Connect

    Sikorski, Johannes; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Saunders, Elizabeth H; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Han, Cliff; Rohde, Manfred; Lang, Elke; Spring, Stefan; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of the cytochrome c nitrite reductase. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    SciTech Connect

    Ivanova, N; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla L.; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Han, Cliff; Detter, J C; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    SciTech Connect

    Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Goker, Markus; Spring, Stefan; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2009-05-20

    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Complete genome sequence of Spirosoma linguale type strain (1T)

    SciTech Connect

    Lail, Kathleen; Sikorski, Johannes; Saunders, Elizabeth H; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Detter, J. Chris; Schutze, Andrea; Rohde, Manfred; Tindall, Brian; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Chen, Feng

    2010-01-01

    Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete ge-nome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plas-mids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacte-ria and Archaea project.

  19. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    PubMed Central

    Ivanova, Natalia; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Saunders, Elizabeth; Han, Cliff; Detter, John C.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304674

  20. Draft genome sequence of Enterococcus faecium strain LMG 8148.

    PubMed

    Michiels, Joran E; Van den Bergh, Bram; Fauvart, Maarten; Michiels, Jan

    2016-01-01

    Enterococcus faecium, traditionally considered a harmless gut commensal, is emerging as an important nosocomial pathogen showing increasing rates of multidrug resistance. We report the draft genome sequence of E. faecium strain LMG 8148, isolated in 1968 from a human in Gothenburg, Sweden. The draft genome has a total length of 2,697,490 bp, a GC-content of 38.3 %, and 2,402 predicted protein-coding sequences. The isolation of this strain predates the emergence of E. faecium as a nosocomial pathogen. Consequently, its genome can be useful in comparative genomic studies investigating the evolution of E. faecium as a pathogen. PMID:27610213

  1. Complete genome sequence of Thermomonospora curvata type strain (B9)

    SciTech Connect

    Chertkov, Olga; Sikorski, Johannes; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Ngatchou, Olivier Duplex; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats

    PubMed Central

    van der Weide, Robin H.; Simonis, Marieke; Hermsen, Roel; Toonen, Pim; Cuppen, Edwin; de Ligt, Joep

    2016-01-01

    Unmapped next-generation sequencing reads are typically ignored while they contain biologically relevant information. We systematically analyzed unmapped reads from whole genome sequencing of 33 inbred rat strains. High quality reads were selected and enriched for biologically relevant sequences; similarity-based analysis revealed clustering similar to previously reported phylogenetic trees. Our results demonstrate that on average 20% of all unmapped reads harbor sequences that can be used to improve reference genomes and generate hypotheses on potential genotype-phenotype relationships. Analysis pipelines would benefit from incorporating the described methods and reference genomes would benefit from inclusion of the genomic segments obtained through these efforts. PMID:27501045

  3. Genome sequencing: a systematic review of health economic evidence

    PubMed Central

    2013-01-01

    Recently the sequencing of the human genome has become a major biological and clinical research field. However, the public health impact of this new technology with focus on the financial effect is not yet to be foreseen. To provide an overview of the current health economic evidence for genome sequencing, we conducted a thorough systematic review of the literature from 17 databases. In addition, we conducted a hand search. Starting with 5 520 records we ultimately included five full-text publications and one internet source, all focused on cost calculations. The results were very heterogeneous and, therefore, difficult to compare. Furthermore, because the methodology of the publications was quite poor, the reliability and validity of the results were questionable. The real costs for the whole sequencing workflow, including data management and analysis, remain unknown. Overall, our review indicates that the current health economic evidence for genome sequencing is quite poor. Therefore, we listed aspects that needed to be considered when conducting health economic analyses of genome sequencing. Thereby, specifics regarding the overall aim, technology, population, indication, comparator, alternatives after sequencing, outcomes, probabilities, and costs with respect to genome sequencing are discussed. For further research, at the outset, a comprehensive cost calculation of genome sequencing is needed, because all further health economic studies rely on valid cost data. The results will serve as an input parameter for budget-impact analyses or cost-effectiveness analyses. PMID:24330507

  4. Complete genome sequence of Staphylothermus hellenicus P8T

    SciTech Connect

    Anderson, Iain; Wirth, Reinhard; Lucas, Susan; Copeland, A; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Davenport, Karen W.; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Hauser, Loren John; Pati, Amrita; Mikhailova, Natalia; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C; Ivanova, N

    2011-01-01

    Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phy- lum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shal- low hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the com- plete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein- coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) La- boratory Sequencing Program (LSP) project.

  5. ICDS database: interrupted CoDing sequences in prokaryotic genomes.

    PubMed

    Perrodou, Emmanuel; Deshayes, Caroline; Muller, Jean; Schaeffer, Christine; Van Dorsselaer, Alain; Ripp, Raymond; Poch, Olivier; Reyrat, Jean-Marc; Lecompte, Odile

    2006-01-01

    Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) that can seriously affect all subsequent steps of functional characterization, from in silico analysis to high-throughput proteomic projects. Here, we describe the Interrupted CoDing Sequence database containing ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes. ICDS can be retrieved by species browsing or similarity searches via a web interface (http://www-bio3d-igbmc.u-strasbg.fr/ICDS/). The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. Furthermore, to facilitate the experimental characterization of ICDS, we propose optimized primers for re-sequencing purposes. The database will be regularly updated with additional data from ongoing sequenced genomes. Our strategy has been validated by three independent tests: (i) ICDS prediction on a benchmark of artificially created frameshifts, (ii) comparison of predicted ICDS and results obtained from the comparison of the two genomic sequences of Bacillus licheniformis strain ATCC 14580 and (iii) re-sequencing of 25 predicted ICDS of the recently sequenced genome of Mycobacterium smegmatis. This allows us to estimate the specificity and sensitivity (95 and 82%, respectively) of our program and the efficiency of primer determination. PMID:16381882

  6. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

    PubMed

    Staats, Martijn; Erkens, Roy H J; van de Vossenberg, Bart; Wieringa, Jan J; Kraaijeveld, Ken; Stielow, Benjamin; Geml, József; Richardson, James E; Bakker, Freek T

    2013-01-01

    Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal

  7. BAC-pool 454-sequencing: A rapid and efficient approach to sequence complex tetraploid cotton genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New and emerging next generation sequencing technologies have been promising in reducing sequencing costs, but not significantly for complex polyploid plant genomes such as cotton. Large and highly repetitive genome of G. hirsutum (~2.5GB) is less amenable and cost-intensive with traditional BAC-by...

  8. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and genomic analyses of Upland cotton (Gossypium hirsutum) are difficult because it has a complex allotetraploid (AADD; 2n = 4x = 52) genome. Here we sequenced, assembled and analyzed the world's most important cultivated cotton genome with 246.2 gigabase (Gb) clean data obtained using whol...

  9. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete sequences of the mitochondrial genomes of the oomycetes Phytophthora ramorum and P. sojae were determined during the course of their complete nuclear genome sequencing (Tyler et al. 2006). Both are circular, with sizes of 39,314 bp for P. ramorum and 42,977 bp for P. sojae. Each contain...

  10. Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect.

    PubMed

    Selvaratnam, Chitra; Thevarajoo, Suganthi; Ee, Robson; Chan, Kok-Gan; Bennett, Joseph P; Goh, Kian Mau; Chong, Chun Shiong

    2016-08-01

    Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain. PMID:27107724

  11. DNA sequence copy number analysis by Comparative Genomic Hybridization (CGH)

    SciTech Connect

    Pinkel, D.; Kallioniemi, A.; Kallioniemi, O.; Waldman, F.; Sudar, D.; Gray, I. ); Rutovitz, D.; Piper, I. )

    1993-01-01

    Comparative Genomic Hybridization (CGH) uses the kinetics of in situ hybridization to compare the copy numbers of different DNA sequences within the same genome and the copy numbers of the same sequences among different genomes. In a typical application genomic DNA from a tumor and from normal cells are differentially labeled and simultaneously hybridized to normal metaphase chromosomes, and detected with different fluorochromes. Properly registered images of each fluorochrome are obtained using a microscope equipped with multi-band filters and a CCD camera. Digital image analysis permits measurement of intensity ratio profiles along each of the target chromosomes. Studies of cells with known aberrations indicate that the intensity ratio at each position is proportional to the ratio of the copy numbers of the sequences that bind there in the tumor and normal genomes. Analytical challenges posed by the need to efficiently obtain copy number karyotypes are discussed.

  12. Complete genome sequence of Cellulomonas flavigena type strain (134T)

    SciTech Connect

    Abt, Birte; Foster, Brian; Lapidus, Alla L.; Clum, Alicia; Sun, Hui; Pukall, Rudiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Genome sequencing and analysis of the model grass Brachypodium distachyon.

    PubMed

    2010-02-11

    Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops. PMID:20148030

  14. The complete chloroplast genome sequence of Zanthoxylum piperitum.

    PubMed

    Lee, Jonghoon; Lee, Hyeon Ju; Kim, Kyunghee; Lee, Sang-Choon; Sung, Sang Hyun; Yang, Tae-Jin

    2016-09-01

    The complete chloroplast genome sequence of Zanthoxylum piperitum, a plant species with useful aromatic oils in family Rutaceae, was generated in this study by de novo assembly with whole-genome sequence data. The chloroplast genome was 158 154 bp in length with a typical quadripartite structure containing a pair of inverted repeats of 27 644 bp, separated by large single copy and small single copy of 85 340 bp and 17 526 bp, respectively. The chloroplast genome harbored 112 genes consisting of 78 protein-coding genes 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences with those of known relatives revealed that Z. piperitum is most closely related to the Citrus species. PMID:26260183

  15. Genome sequencing and analysis of the model grass Brachypodium distachyon

    SciTech Connect

    Yang, Xiaohan; Kalluri, Udaya C; Tuskan, Gerald A

    2010-01-01

    Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

  16. The Release 6 reference sequence of the Drosophila melanogaster genome

    DOE PAGESBeta

    Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; Park, Soo; Mendez, Ivonne; Galle, Samuel E.; Booth, Benjamin W.; Pfeiffer, Barret D.; George, Reed A.; Svirskas, Robert; et al

    2015-01-14

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

  17. The Release 6 reference sequence of the Drosophila melanogaster genome

    PubMed Central

    Carlson, Joseph W.; Wan, Kenneth H.; Park, Soo; Mendez, Ivonne; Galle, Samuel E.; Booth, Benjamin W.; Pfeiffer, Barret D.; George, Reed A.; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V.; Andreyeva, Evgeniya N.; Boldyreva, Lidiya V.; Marra, Marco; Carvalho, A. Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F.; Rubin, Gerald M.; Karpen, Gary H.

    2015-01-01

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. PMID:25589440

  18. The Release 6 reference sequence of the Drosophila melanogaster genome.

    PubMed

    Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

    2015-03-01

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. PMID:25589440

  19. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

    SciTech Connect

    Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

    2011-04-29

    In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

  20. Perspectives of integrative cancer genomics in next generation sequencing era.

    PubMed

    Kwon, So Mee; Cho, Hyunwoo; Choi, Ji Hye; Jee, Byul A; Jo, Yuna; Woo, Hyun Goo

    2012-06-01

    The explosive development of genomics technologies including microarrays and next generation sequencing (NGS) has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research. PMID:23105932

  1. The complete chloroplast genome sequence of Panax quinquefolius (L.).

    PubMed

    Kim, Kyunghee; Lee, Sang-Choon; Lee, Junki; Kim, Nam-Hoon; Jang, Woojong; Yang, Tae-Jin

    2016-07-01

    The complete chloroplast genome sequence of Panax quinquefolius, an important medicinal herb, was generated by de novo assembly with low-coverage whole-genome sequence data and manual correction. A circular 156 088-bp chloroplast genome showed typical chloroplast genome structure comprising a large single copy region of 86 095 bp, a small single copy region of 17 993 bp, and a pair of inverted repeats of 26 000 bp. The chloroplast genome had 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis with the chloroplast genome revealed that P. quinquefolius is much closer to P. ginseng than P. notoginseng. PMID:26162051

  2. Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762

    PubMed Central

    Gradnigo, Julien S.; Somerville, Greg A.; Huether, Michael J.; Kemmy, Richard J.; Johnson, Craig M.; Oliver, Michael G.

    2016-01-01

    Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracycline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain 10762. PMID:27340076

  3. Complete genome sequence of Allochromatium vinosum DSM 180T

    PubMed Central

    Weissgerber, Thomas; Zigann, Renate; Bruce, David; Chang, Yun-juan; Detter, John C.; Han, Cliff; Hauser, Loren; Jeffries, Cynthia D.; Land, Miriam; Munk, A. Christine; Tapia, Roxanne; Dahl, Christiane

    2011-01-01

    Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacterium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains currently five species. All members were isolated from freshwater, brackish water or marine habitats and are predominately obligate phototrophs. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the Chromatiaceae within the purple sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp genome with its 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Genome Institute Community Sequencing Program. PMID:22675582

  4. Draft Genome Sequence of Paecilomyces hepiali, Isolated from Cordyceps sinensis.

    PubMed

    Yu, Yi; Wang, Wenting; Wang, Linping; Pang, Fang; Guo, Lanping; Song, Lai; Liu, Guiming; Feng, Chengqiang

    2016-01-01

    Paecilomyces hepiali is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis Here, we report the draft genome sequence of P. hepiali, which will facilitate the exploitation of medicinal compounds produced by the fungus. PMID:27389266

  5. Complete Genome Sequence of Rahnella aquatilis CIP 78.65

    PubMed Central

    Bruce, David; Detter, Chris; Goodwin, Lynne A.; Han, James; Han, Cliff S.; Held, Brittany; Land, Miriam L.; Mikhailova, Natalia; Nolan, Matt; Pennacchio, Len; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Sobecky, Patricia A.

    2012-01-01

    Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65, the type strain of R. aquatilis. PMID:22582378

  6. Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195

    PubMed Central

    Gueimonde, Miguel; Ventura, Marco; Margolles, Abelardo

    2012-01-01

    In this work, we report the genome sequences of Bifidobacterium bifidum strain LMG13195. Results from our research group show that this strain is able to interact with human immune cells, generating functional regulatory T cells. PMID:23209243

  7. Draft Genome Sequence of Lactobacillus plantarum Strain IPLA 88

    PubMed Central

    Ladero, Victor; Alvarez-Sieiro, Patricia; Redruello, Begoña; del Rio, Beatriz; Linares, Daniel M.; Martin, M. Cruz; Fernández, María

    2013-01-01

    Here, we report a 3.2-Mbp draft assembly for the genome of Lactobacillus plantarum IPLA 88. The sequence of this sourdough isolate provides insight into the adaptation of this versatile species to different environments. PMID:23887921

  8. Sequence analysis of the complete mitochondrial genome of Youxian sheldrake.

    PubMed

    He, Shao-Ping; Liu, Li-Li; Yu, Qi-Fang; Li, Si; He, Jian-Hua

    2016-01-01

    Youxian sheldrake is excellent native breeds in Hunan province in China. The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. This is the first study to determine the complete mitochondrial genome sequence of Youxian sheldrake using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, the total length of the mitogenome is 16,605 bp, with the base composition of 29.21% A, 22.18% T, 32.84% C, 15.77% G in the Youxian sheldrake. It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Youxian sheldrake provided an important data for further study of the phylogenetics of poultry, and available data for the genetics and breeding. PMID:25090395

  9. Complete Genome Sequences of Six Strains of the Genus Methylobacterium

    SciTech Connect

    Marx, Christopher J; Bringel, Francoise O.; Christoserdova, Ludmila; Moulin, Lionel; UI Hague, Muhammad Farhan; Fleischman, Darrell E.; Gruffaz, Christelle; Jourand, Philippe; Knief, Claudia; Lee, Ming-Chun; Muller, Emilie E. L.; Nadalig, Thierry; Peyraud, Remi; Roselli, Sandro; Russ, Lina; Goodwin, Lynne A.; Ivanov, Pavel S.; Ivanova, N; Kyrpides, Nikos C; Lajus, Aurelie; Medigue, Claudine; Nolan, Matt; Woyke, Tanja; Stolyar, Sergey; Vorholt, Julia A.; Vuilleumier, Stephane

    2012-01-01

    The complete and assembled genome sequences were determined for six strains of the alphaproteobacterial genus Methylobacterium, chosen for their key adaptations to different plant-associated niches and environmental constraints.

  10. Complete genome sequences of six strains of the genus methylobacterium

    SciTech Connect

    Marx, Christopher J; Bringel, Francoise O.; Christoserdova, Ludmila; Moulin, Lionel; Farhan Ul Haque, Muhammad; Fleischman, Darrell E.; Gruffaz, Christelle; Jourand, Philippe; Knief, Claudia; Lee, Ming-Chun; Muller, Emilie E. L.; Nadalig, Thierry; Peyraud, Remi; Roselli, Sandro; Russ, Lina; Aguero, Fernan; Goodwin, Lynne A.; Ivanova, N; Kyrpides, Nikos C; Lajus, Aurelie; Medigue, Claudine; Nolan, Matt; Woyke, Tanja; Stolyar, Sergey; Vorholt, Julia A.; Vuilleumier, Stephane

    2012-01-01

    The complete and assembled genome sequences were determined for six strains of the alphaproteobacterial genus Methylobacterium, chosen for their key adaptations to different plant-associated niches and environmental constraints.

  11. Bacterial epidemiology and biology - lessons from genome sequencing

    PubMed Central

    2011-01-01

    Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution. PMID:22027015

  12. Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila JBN2301.

    PubMed

    Yang, Wuming; Li, Ningqiu; Li, Ming; Zhang, Defeng; An, Guannan

    2016-01-01

    Aeromonas hydrophila is one of the most important fish pathogens in China. Here, we report complete genome sequence of a virulent strain, A. hydrophila JBN2301, which was isolated from diseased crucian carp. PMID:26823580

  13. Complete Genome Sequence of Rahnella aquatilis CIP 78.65

    SciTech Connect

    Martinez, Robert J; Bruce, David; Detter, J C; Goodwin, Lynne A.; Han, James; Han, Cliff; Held, Brittany; Land, Miriam L; Mikhailova, Natalia; Nolan, Matt; Pennacchio, Len; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Sobeckya, Patricia A.

    2012-01-01

    Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65, the type strain of R. aquatilis.

  14. Draft Genome Sequence of Lactobacillus casei W56

    PubMed Central

    Hochwind, Kerstin; Weinmaier, Thomas; Schmid, Michael; van Hemert, Saskia; Hartmann, Anton; Rattei, Thomas

    2012-01-01

    We announce the draft genome sequence of Lactobacillus casei W56 in one contig. This strain shows immunomodulatory and probiotic properties. The strain is also an ingredient of commercially available probiotic products. PMID:23144392

  15. Draft genome sequence of Lactobacillus casei W56.

    PubMed

    Hochwind, Kerstin; Weinmaier, Thomas; Schmid, Michael; van Hemert, Saskia; Hartmann, Anton; Rattei, Thomas; Rothballer, Michael

    2012-12-01

    We announce the draft genome sequence of Lactobacillus casei W56 in one contig. This strain shows immunomodulatory and probiotic properties. The strain is also an ingredient of commercially available probiotic products. PMID:23144392

  16. Genome sequence of the fish pathogen Flavobacterium columnare ATCC 49512

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flavobacterium columnare is a Gram-negative, rod shaped, motile, and highly prevalent fish pathogen causing columnaris disease in freshwater fish worldwide. Here, we present the complete genome sequence of F. columnare strain ATCC 49512. ...

  17. First Draft Genome Sequence of a Mycobacterium gordonae Clinical Isolate

    PubMed Central

    Smirnova, T.; Blagodatskikh, K.; Varlamov, D.; Sochivko, D.; Larionova, E.; Andreevskaya, S.; Andrievskaya, I.; Chernousova, L.

    2016-01-01

    Here, we report the first draft genome sequence of the clinically relevant species Mycobacterium gordonae. The clinical isolate Mycobacterium gordonae 14-8773 was obtained from the sputum of a patient with mycobacteriosis. PMID:27365356

  18. Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila JBN2301

    PubMed Central

    Yang, Wuming; Li, Ming; Zhang, Defeng; An, Guannan

    2016-01-01

    Aeromonas hydrophila is one of the most important fish pathogens in China. Here, we report complete genome sequence of a virulent strain, A. hydrophila JBN2301, which was isolated from diseased crucian carp. PMID:26823580

  19. Draft Genome Sequence of Pseudomonas syringae pv. persicae NCPPB 2254.

    PubMed

    Zhao, Wenjun; Jiang, Hongshan; Tian, Qian; Hu, Jie

    2015-01-01

    Pseudomonas syringae pv. persicae is a pathogen that causes bacterial decline of stone fruit. Here, we report the draft genome sequence for P. syringae pv. persicae, which was isolated from Prunus persica. PMID:26044420

  20. Cancer Genome Sequencing and Its Implications for Personalized Cancer Vaccines

    PubMed Central

    Li, Lijin; Goedegebuure, Peter; Mardis, Elaine R.; Ellis, Matthew J.C.; Zhang, Xiuli; Herndon, John M.; Fleming, Timothy P.; Carreno, Beatriz M.; Hansen, Ted H.; Gillanders, William E.

    2011-01-01

    New DNA sequencing platforms have revolutionized human genome sequencing. The dramatic advances in genome sequencing technologies predict that the $1,000 genome will become a reality within the next few years. Applied to cancer, the availability of cancer genome sequences permits real-time decision-making with the potential to affect diagnosis, prognosis, and treatment, and has opened the door towards personalized medicine. A promising strategy is the identification of mutated tumor antigens, and the design of personalized cancer vaccines. Supporting this notion are preliminary analyses of the epitope landscape in breast cancer suggesting that individual tumors express significant numbers of novel antigens to the immune system that can be specifically targeted through cancer vaccines. PMID:24213133

  1. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.

    PubMed

    Flynn, James D; Hirayama, Hisako; Sakai, Yasuyoshi; Dunfield, Peter F; Klotz, Martin G; Knief, Claudia; Op den Camp, Huub J M; Jetten, Mike S M; Khmelenina, Valentina N; Trotsenko, Yuri A; Murrell, J Colin; Semrau, Jeremy D; Svenning, Mette M; Stein, Lisa Y; Kyrpides, Nikos; Shapiro, Nicole; Woyke, Tanja; Bringel, Françoise; Vuilleumier, Stéphane; DiSpirito, Alan A; Kalyuzhnaya, Marina G

    2016-01-01

    The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems. PMID:26798114

  2. Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems

    PubMed Central

    Flynn, James D.; Hirayama, Hisako; Sakai, Yasuyoshi; Dunfield, Peter F.; Knief, Claudia; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Khmelenina, Valentina N.; Trotsenko, Yuri A.; Murrell, J. Colin; Semrau, Jeremy D.; Svenning, Mette M.; Stein, Lisa Y.; Kyrpides, Nikos; Shapiro, Nicole; Woyke, Tanja; Bringel, Françoise; Vuilleumier, Stéphane; DiSpirito, Alan A.

    2016-01-01

    The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems. PMID:26798114

  3. Draft Genome Sequence of Paecilomyces hepiali, Isolated from Cordyceps sinensis

    PubMed Central

    Yu, Yi; Wang, Wenting; Wang, Linping; Pang, Fang; Guo, Lanping; Song, Lai

    2016-01-01

    Paecilomyces hepiali is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis. Here, we report the draft genome sequence of P. hepiali, which will facilitate the exploitation of medicinal compounds produced by the fungus. PMID:27389266

  4. Genome sequence of vanilla distortion mosaic virus infecting Coriandrum sativum.

    PubMed

    Adams, I P; Rai, S; Deka, M; Harju, V; Hodges, T; Hayward, G; Skelton, A; Fox, A; Boonham, N

    2014-12-01

    The 9573-nucleotide genome of a potyvirus was sequenced from a Coriandrum sativum plant from India with viral symptoms. On analysis, this virus was shown to have greater than 85 % nucleotide sequence identity to vanilla distortion mosaic virus (VDMV). Analysis of the putative coat protein sequence confirmed that this virus was in fact VDMV, with greater than 91 % amino acid sequence identity. The genome appears to encode a 3083-amino-acid polyprotein potentially cleaved into the 10 mature proteins expected in potyviruses. Phylogenetic analysis confirmed that VDMV is a distinct but ungrouped member of the genus Potyvirus. PMID:25252813

  5. Complete genome sequence of Treponema pallidum strain DAL-1

    PubMed Central

    Zobaníková, Marie; Mikolka, Pavol; Čejková, Darina; Pospíšilová, Petra; Chen, Lei; Strouhal, Michal; Qin, Xiang; Weinstock, George M.; Šmajs, David

    2012-01-01

    Treponema pallidum strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant woman in the secondary stage of syphilis. Here we describe the 1,139,971 bp long genome of T. pallidum strain DAL-1 which was sequenced using two independent sequencing methods (454 pyrosequencing and Illumina). In rabbits, strain DAL-1 replicated better than the T. pallidum strain Nichols. The comparison of the complete DAL-1 genome sequence with the Nichols sequence revealed a list of genetic differences that are potentially responsible for the increased rabbit virulence of the DAL-1 strain. PMID:23449808

  6. Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7.

    PubMed

    Rey, Andrés; Silva-Quintero, Laura; Dussán, Jenny

    2016-09-01

    Lysinibacillus sphaericus III(3)7 is a native Colombian strain, the first one isolated from soil samples. This strain has shown high levels of pathogenic activity against Culex quinquefaciatus larvae in laboratory assays compared to other members of the same species. Using Pacific Biosciences sequencing technology we sequenced, annotated (de novo) and described the genome of strain III(3)7, achieving a complete genome sequence status. We then performed a comparative analysis between the newly sequenced genome and the ones previously reported for Colombian isolates L. sphaericus OT4b.31, CBAM5 and OT4b.25, with the inclusion of L. sphaericus C3-41 that has been used as a reference genome for most of previous genome sequencing projects. We concluded that L. sphaericus III(3)7 is highly similar with strain OT4b.25 and shares high levels of synteny with isolates CBAM5 and C3-41. PMID:27419068

  7. Intra-species sequence comparisons for annotating genomes

    SciTech Connect

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  8. Draft genome sequence of Therminicola potens strain JR

    SciTech Connect

    Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C.; Coates, J.D.

    2010-07-01

    'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.

  9. Draft Genome Sequence of Lactobacillus fermentum Strain 3872

    PubMed Central

    Raju, Kavita; Abramov, Vyacheslav M.

    2013-01-01

    This report describes a draft genome sequence of Lactobacillus fermentum strain 3872. The data revealed remarkable similarity to and dissimilarity with the published genome sequences of other strains of the species. The absence of and variation in structures of some adhesins and the presence of an additional adhesin may reflect adaptation of the bacterium to different host systems and may contribute to specific properties of this strain as a new probiotic. PMID:24285652

  10. Whole Genome and Transcriptome Sequencing of a B3 Thymoma

    PubMed Central

    Petrini, Iacopo; Rajan, Arun; Pham, Trung; Voeller, Donna; Davis, Sean; Gao, James; Wang, Yisong; Giaccone, Giuseppe

    2013-01-01

    Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive sequencing has been reported in thymomas. Here we present the first comprehensive view of a B3 thymoma at whole genome and transcriptome levels. A 55-year-old Caucasian female underwent complete resection of a stage IVA B3 thymoma. RNA and DNA were extracted from a snap frozen tumor sample with a fraction of cancer cells over 80%. We performed array comparative genomic hybridization using Agilent platform, transcriptome sequencing using HiSeq 2000 (Illumina) and whole genome sequencing using Complete Genomics Inc platform. Whole genome sequencing determined, in tumor and normal, the sequence of both alleles in more than 95% of the reference genome (NCBI Build 37). Copy number (CN) aberrations were comparable with those previously described for B3 thymomas, with CN gain of chromosome 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. One translocation t(11;X) was identified by whole genome sequencing and confirmed by PCR and Sanger sequencing. Ten single nucleotide variations (SNVs) and 2 insertion/deletions (INDELs) were identified; these mutations resulted in non-synonymous amino acid changes or affected splicing sites. The lack of common cancer-associated mutations in this patient suggests that thymomas may evolve through mechanisms distinctive from other tumor types, and supports the rationale for additional high-throughput sequencing screens to better understand the somatic genetic architecture of thymoma. PMID:23577124

  11. A computational genomics pipeline for prokaryotic sequencing projects

    PubMed Central

    Kislyuk, Andrey O.; Katz, Lee S.; Agrawal, Sonia; Hagen, Matthew S.; Conley, Andrew B.; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C.; Sammons, Scott A.; Govil, Dhwani; Mair, Raydel D.; Tatti, Kathleen M.; Tondella, Maria L.; Harcourt, Brian H.; Mayer, Leonard W.; Jordan, I. King

    2010-01-01

    Motivation: New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. Availability and implementation: The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems. Contact: king.jordan@biology.gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20519285

  12. Genome Sequence of Pantoea agglomerans Strain IG1

    PubMed Central

    Matsuzawa, Tomohiko; Mori, Kazuki; Kadowaki, Takeshi; Shimada, Misato; Tashiro, Kosuke; Kuhara, Satoru; Inagawa, Hiroyuki; Soma, Gen-ichiro

    2012-01-01

    Pantoea agglomerans is a Gram-negative bacterium that grows symbiotically with various plants. Here we report the 4.8-Mb genome sequence of P. agglomerans strain IG1. The lipopolysaccharides derived from P. agglomerans IG1 have been shown to be effective in the prevention of various diseases, such as bacterial or viral infection, lifestyle-related diseases. This genome sequence represents a substantial step toward the elucidation of pathways for production of lipopolysaccharides. PMID:22328756

  13. Draft genome sequence of Gluconobacter thailandicus NBRC 3257

    PubMed Central

    Matsutani, Minenosuke; Yakushi, Toshiharu

    2014-01-01

    Gluconobacter thailandicus strain NBRC 3257, isolated from downy cherry (Prunus tomentosa), is a strict aerobic rod-shaped Gram-negative bacterium. Here, we report the features of this organism, together with the draft genome sequence and annotation. The draft genome sequence is composed of 107 contigs for 3,446,046 bp with 56.17% G+C content and contains 3,360 protein-coding genes and 54 RNA genes. PMID:25197448

  14. Draft Genome Sequence of Rhodococcus sp. Strain 311R

    PubMed Central

    Ehsani, Elham; Jauregui, Ruy; Geffers, Robert; Jareck, Michael; Boon, Nico; Pieper, Dietmar H.

    2015-01-01

    Here, we report the draft genome sequence of Rhodococcus sp. strain 311R, which was isolated from a site contaminated with alkanes and aromatic compounds. Strain 311R shares 90% of the genome of Rhodococcus erythropolis SK121, which is the closest related bacteria. PMID:25999565

  15. Draft Genome Sequence of Mycobacterium vulneris DSM 45247T

    PubMed Central

    Croce, Olivier; Robert, Catherine; Raoult, Didier

    2014-01-01

    We report the draft genome sequence of Mycobacterium vulneris DSM 45247T strain, an emerging, opportunistic pathogen of the Mycobacterium avium complex. The genome described here is composed of 6,981,439 bp (with a G+C content of 67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes. PMID:24812218

  16. Draft Genome Sequence of Mycobacterium vulneris DSM 45247T.

    PubMed

    Croce, Olivier; Robert, Catherine; Raoult, Didier; Drancourt, Michel

    2014-01-01

    We report the draft genome sequence of Mycobacterium vulneris DSM 45247(T) strain, an emerging, opportunistic pathogen of the Mycobacterium avium complex. The genome described here is composed of 6,981,439 bp (with a G+C content of 67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes. PMID:24812218

  17. Genome Sequence of Type Strain Lysinibacillus macroides DSM 54T

    PubMed Central

    Liu, Guo-hong; Wang, Jie-ping; Che, Jian-Mei; Chen, Qian-Qian; Chen, Zheng; Ge, Ci-bin

    2015-01-01

    Lysinibacillus macroides DSM 54T is a Gram-positive, spore-forming bacterium. Here, we report the 4,866,035-bp genome sequence of Lysinibacillus macroides DSM 54T, which will accelerate the application of degrading xylan and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26543111

  18. Complete Genome Sequence of Mycoplasma synoviae Strain WVU 1853T

    PubMed Central

    Kutish, Gerald F.; Barbet, Anthony F.; Michaels, Dina L.

    2015-01-01

    A hybrid sequence assembly of the complete Mycoplasma synoviae type strain WVU 1853T genome was compared to that of strain MS53. The findings support prior conclusions about M. synoviae, based on the genome of that otherwise uncharacterized field strain, and provide the first evidence of epigenetic modifications in M. synoviae. PMID:26021934

  19. Whole-genome sequences of three symbiotic endozoicomonas strains.

    PubMed

    Neave, Matthew J; Michell, Craig T; Apprill, Amy; Voolstra, Christian R

    2014-01-01

    Members of the genus Endozoicomonas associate with a wide range of marine organisms. Here, we report on the whole-genome sequencing, assembly, and annotation of three Endozoicomonas type strains. These data will assist in exploring interactions between Endozoicomonas organisms and their hosts, and it will aid in the assembly of genomes from uncultivated Endozoicomonas spp. PMID:25125646

  20. Whole-Genome Sequences of Three Symbiotic Endozoicomonas Bacteria

    PubMed Central

    Neave, Matthew J.; Michell, Craig T.

    2014-01-01

    Members of the genus Endozoicomonas associate with a wide range of marine organisms. Here, we report on the whole-genome sequencing, assembly, and annotation of three Endozoicomonas type strains. These data will assist in exploring interactions between Endozoicomonas organisms and their hosts, and it will aid in the assembly of genomes from uncultivated Endozoicomonas spp. PMID:25125646

  1. Response to 'pervasive sequence patents cover the entire human genome'.

    PubMed

    Tu, Shine; Holman, Christopher; Mossoff, Adam; Sichelman, Ted; Risch, Michael; Conteras, Jorge L; Heled, Yaniv; Dolin, Greg; Petherbridge, Lee

    2014-01-01

    A response to Pervasive sequence patents cover the entire human genome by J Rosenfeld and C Mason. Genome Med 2013, 5:27. See related Correspondence by Rosenfeld and Mason, http://genomemedicine.com/content/5/3/27 and related letter by Rosenfeld and Mason, http://genomemedicine.com/content/6/2/15. PMID:25031614

  2. Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge.

    PubMed

    Cornell, Jessica L; Breslin, Eileen; Schuhmacher, Zachary; Himelright, Madison; Berluti, Cassandra; Boyd, Charles; Carson, Rachel; Del Gallo, Elle; Giessler, Caris; Gilliam, Benjamin; Heatherly, Catherine; Nevin, Julius; Nguyen, Bryan; Nguyen, Justin; Parada, Jocelyn; Sutterfield, Blake; Tukruni, Muruj; Temple, Louise

    2016-01-01

    Smudge, a bacteriophage enriched from soil using Bacillus thuringiensis DSM-350 as the host, had its complete genome sequenced. Smudge is a myovirus with a genome consisting of 292 genes and was identified as belonging to the C1 cluster of Bacillus phages. PMID:27540049

  3. Complete Genome Sequence of the Oncolytic Sendai virus Strain Moscow.

    PubMed

    Zainutdinov, Sergei S; Tikunov, Artem Y; Matveeva, Olga V; Netesov, Sergei V; Kochneva, Galina V

    2016-01-01

    We report here the complete genome sequence of Sendai virus Moscow strain. Anecdotal evidence for the efficacy of oncolytic virotherapy exists for this strain. The RNA genome of the Moscow strain is 15,384 nucleotides in length and differs from the nearest strain, BB1, by 18 nucleotides and 11 amino acids. PMID:27516510

  4. Complete Genome Sequence of the Oncolytic Sendai virus Strain Moscow

    PubMed Central

    Zainutdinov, Sergei S.; Tikunov, Artem Y.; Matveeva, Olga V.

    2016-01-01

    We report here the complete genome sequence of Sendai virus Moscow strain. Anecdotal evidence for the efficacy of oncolytic virotherapy exists for this strain. The RNA genome of the Moscow strain is 15,384 nucleotides in length and differs from the nearest strain, BB1, by 18 nucleotides and 11 amino acids. PMID:27516510

  5. Complete genome sequence of Aeromonas hydrophila AL06-06

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aeromonas hydrophila occurs in freshwater environments and infects fish and mammals. In this work, we report the complete genome sequence of Aeromonas hydrophila AL06-06, which was isolated from diseased goldfish and is being used for comparative genomic studies with A. hydrophila strains causing ba...

  6. Complete Genome Sequence of Klebsiella pneumoniae YH43.

    PubMed

    Iwase, Tadayuki; Ogura, Yoshitoshi; Hayashi, Tetsuya; Mizunoe, Yoshimitsu

    2016-01-01

    We report here the complete genome sequence ofKlebsiella pneumoniaestrain YH43, isolated from sweet potato. The genome consists of a single circular chromosome of 5,520,319 bp in length. It carries 8 copies of rRNA operons, 86 tRNA genes, 5,154 protein-coding genes, and thenifgene cluster for nitrogen fixation. PMID:27081127

  7. Draft Genome Sequence of "Candidatus Liberibacter asiaticus" from California.

    PubMed

    Zheng, Z; Deng, X; Chen, J

    2014-01-01

    We report here the draft genome sequence of "Candidatus Liberibacter asiaticus" strain HHCA, collected from a lemon tree in California. The HHCA strain has a genome size of 1,150,620 bp, 36.5% G+C content, 1,119 predicted open reading frames, and 51 RNA genes. PMID:25278540

  8. Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829

    PubMed Central

    Croce, Olivier; Robert, Catherine; Raoult, Didier

    2014-01-01

    We announce the draft genome sequence of Mycobacterium cosmeticum strain DSM 44829, a nontuberculous species responsible for opportunistic infection. The genome described here is composed of 6,462,090 bp, with a G+C content of 68.24%. It contains 6,281 protein-coding genes and 75 predicted RNA genes. PMID:24723727

  9. Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1

    PubMed Central

    Andrade-Domínguez, Andrés

    2016-01-01

    Aspects of the interaction between phages and animals are of interest and importance for medical applications. Here, we report the genome sequence of the lytic Pseudomonas phage AAT-1, isolated from mammalian serum. AAT-1 is a double-stranded DNA phage, with a genome of 57,599 bp, containing 76 predicted open reading frames. PMID:27563032

  10. A snapshot of the emerging tomato genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the ‘International Solanaceae Genome Proje...

  11. Whole-Genome Sequence of Staphylococcus epidermidis Tü3298

    PubMed Central

    Moran, Josephine C.

    2016-01-01

    Staphylococcus epidermidis Tü3298 is a frequently used laboratory strain, known for its production of epidermin and absence of the icaABCD operon. We report the whole-genome sequence of this strain, a 2.5-kb genome containing 2,332 genes. PMID:26966218

  12. Complete Genome Sequence of Mycobacterium bovis Strain BCG-1 (Russia)

    PubMed Central

    Shitikov, Egor A.; Malakhova, Maja V.; Kostryukova, Elena S.; Ilina, Elena N.; Atrasheuskaya, Alena V.; Ignatyev, Georgy M.; Vinokurova, Nataliya V.; Gorbachyov, Vyacheslav Y.

    2016-01-01

    Mycobacterium bovis BCG (Bacille Calmette-Guérin) is a vaccine strain used for protection against tuberculosis. Here, we announce the complete genome sequence of M. bovis strain BCG-1 (Russia). Extensive use of this strain necessitates the study of its genome stability by comparative analysis. PMID:27034492

  13. Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1.

    PubMed

    Andrade-Domínguez, Andrés; Kolter, Roberto

    2016-01-01

    Aspects of the interaction between phages and animals are of interest and importance for medical applications. Here, we report the genome sequence of the lytic Pseudomonas phage AAT-1, isolated from mammalian serum. AAT-1 is a double-stranded DNA phage, with a genome of 57,599 bp, containing 76 predicted open reading frames. PMID:27563032

  14. Complete Genome Sequence of Mycobacterium bovis Strain BCG-1 (Russia).

    PubMed

    Sotnikova, Evgeniya A; Shitikov, Egor A; Malakhova, Maja V; Kostryukova, Elena S; Ilina, Elena N; Atrasheuskaya, Alena V; Ignatyev, Georgy M; Vinokurova, Nataliya V; Gorbachyov, Vyacheslav Y

    2016-01-01

    Mycobacterium bovisBCG (Bacille Calmette-Guérin) is a vaccine strain used for protection against tuberculosis. Here, we announce the complete genome sequence ofM. bovisstrain BCG-1 (Russia). Extensive use of this strain necessitates the study of its genome stability by comparative analysis. PMID:27034492

  15. Genome Sequence of Xanthomonas citri pv. mangiferaeindicae Strain LMG 941

    PubMed Central

    Midha, Samriti; Ranjan, Manish; Sharma, Vikas; Pinnaka, Anil Kumar

    2012-01-01

    We report the 5.1-Mb genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG 941, the causal agent of bacterial black spot in mango. Apart from evolutionary studies, the draft genome will be a valuable resource for the epidemiological studies and quarantine of this phytopathogen. PMID:22582385

  16. The tomato genome sequence provides insight into fleshy fruit evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the inbred tomato cultivar ‘Heinz 1706’ was sequenced and assembled using a combination of Sanger and “next generation” technologies. The predicted genome size is ~900 Mb, consistent with prior estimates, of which 760 Mb were assembled in 91 scaffolds aligned to the 12 tomato chromosom...

  17. Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga Cymbomonas tetramitiformis

    PubMed Central

    Paasch, Amber E.; Graham, Linda E.; Kim, Eunsoo

    2016-01-01

    We report here the complete chloroplast genome sequence of Cymbomonas tetramitiformis strain PLY262, which is a prasinophycean green alga that retains a phagomixotrophic mode of nutrition. The genome is 84,524 bp in length, with a G+C content of 37%, and contains 3 rRNAs, 26 tRNAs, and 76 protein-coding genes. PMID:27313295

  18. Complete genome sequence of Campylobacter gracilis ATCC 33236T

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The human oral pathogen Campylobacter gracilis has been isolated from periodontal and endodontal infections, and also from non-oral head, neck or lung infections. This study describes the whole-genome sequence of the human periodontal isolate ATCC 33236T (=FDC 1084), which is the first closed genome...

  19. Complete genome sequence of pronghorn virus, a pestivirus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genome sequence of Pronghorn virus, a member of the Pestivirus genus of the Flaviviridae, was determined. The virus, originally isolated from a pronghorn antelope, had a genome of 12,287 nucleotides with a single open reading frame of 11,694 bases encoding 3898 amino acids....

  20. Draft genome sequence of Phomopsis longicolla MSPL 10-6

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phomopsis longicolla T.W. Hobbs is the primary cause of Phomopsis seed decay in soybean. We report the de novo assembled draft genome sequence of P. longicolla isolate MSPL10-6 with a 54.8-fold depth of coverage. The resulting draft genome was estimated to be approximately 64 Mb in size with an over...

  1. Genome sequence of the cultivated cotton Gossypium arboreum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton is one of the most economically important natural fiber crops in the world, and the complex tetraploid nature of its genome (AADD, 2n = 52) makes genetic, genomic and functional analyses extremely challenging. Here we sequenced and assembled 98.3% of the 1.7-gigabase G. arboreum (AA, 2n = 26...

  2. First Complete Genome Sequence of Felis catus Gammaherpesvirus 1

    PubMed Central

    Lee, Justin S.; Vuyisich, Momchilo; Chain, Patrick; Lo, Chien-Chi; Kronmiller, Brent; Bracha, Shay; Avery, Anne C.; VandeWoude, Sue

    2015-01-01

    We sequenced the complete genome of Felis catus gammaherpesvirus 1 (FcaGHV1) from lymph node DNA of an infected cat. The genome includes a 121,556-nucleotide unique region with 87 predicted open reading frames (61 gammaherpesvirus conserved and 26 unique) flanked by multiple copies of a 966-nucleotide terminal repeat. PMID:26543105

  3. Complete Genome Sequence of Cyanobacterial Siphovirus KBS2A.

    PubMed

    Ponsero, Alise J; Chen, Feng; Lennon, Jay T; Wilhelm, Steven W

    2013-01-01

    We present the genome of a cyanosiphovirus (KBS2A) that infects a marine Synechococcus sp. (strain WH7803). Unique to this genome, relative to other sequenced cyanosiphoviruses, is the absence of elements associated with integration into the host chromosome, suggesting this virus may not be able to establish a lysogenic relationship. PMID:23969045

  4. Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G

    PubMed Central

    Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng

    2013-01-01

    Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus. PMID:24051316

  5. Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755

    PubMed Central

    Fujisawa, Takatomo; Ohtsubo, Yoshiyuki; Katayama, Mitsunori; Misawa, Naomi; Wakazuki, Sachiko; Shimura, Yohei; Nakamura, Yasukazu; Kawachi, Masanobu; Yoshikawa, Hirofumi; Eki, Toshihiko

    2016-01-01

    Cyanobacterial genus Leptolyngbya comprises genetically diverse species, but the availability of their complete genome information is limited. Here, we isolated Leptolyngbya sp. strain NIES-3755 from soil at the Toyohashi University of Technology, Japan. We determined the complete genome sequence of the NIES-3755 strain, which is composed of one chromosome and three plasmids. PMID:26988037

  6. Draft Genome Sequence of Bacillus tequilensis Strain FJAT-14262a

    PubMed Central

    Chen, Qian-Qian; Liu, Guo-hong; Wang, Jie-ping; Che, Jian-Mei

    2015-01-01

    Bacillus tequilensis FJAT-14262a is a Gram-positive rod-shaped bacterium. Here, we report the 4,038,551-bp genome sequence of B. tequilensis FJAT-14262a, which will provide useful information for genomic taxonomy and phylogenomics of Bacillus. PMID:26564040

  7. Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge

    PubMed Central

    Cornell, Jessica L.; Breslin, Eileen; Schuhmacher, Zachary; Himelright, Madison; Berluti, Cassandra; Boyd, Charles; Carson, Rachel; Del Gallo, Elle; Giessler, Caris; Gilliam, Benjamin; Heatherly, Catherine; Nevin, Julius; Nguyen, Bryan; Nguyen, Justin; Parada, Jocelyn; Sutterfield, Blake; Tukruni, Muruj

    2016-01-01

    Smudge, a bacteriophage enriched from soil using Bacillus thuringiensis DSM-350 as the host, had its complete genome sequenced. Smudge is a myovirus with a genome consisting of 292 genes and was identified as belonging to the C1 cluster of Bacillus phages. PMID:27540049

  8. Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga Cymbomonas tetramitiformis.

    PubMed

    Satjarak, Anchittha; Paasch, Amber E; Graham, Linda E; Kim, Eunsoo

    2016-01-01

    We report here the complete chloroplast genome sequence of Cymbomonas tetramitiformis strain PLY262, which is a prasinophycean green alga that retains a phagomixotrophic mode of nutrition. The genome is 84,524 bp in length, with a G+C content of 37%, and contains 3 rRNAs, 26 tRNAs, and 76 protein-coding genes. PMID:27313295

  9. Complete Mitochondrial Genome Sequence of the Pezizomycete Pyronema confluens

    PubMed Central

    2016-01-01

    The complete mitochondrial genome of the ascomycete Pyronema confluens has been sequenced. The circular genome has a size of 191 kb and contains 48 protein-coding genes, 26 tRNA genes, and two rRNA genes. Of the protein-coding genes, 14 encode conserved mitochondrial proteins, and 31 encode predicted homing endonuclease genes. PMID:27174271

  10. Genomic sequence for the aflatoxigenic filamentous fungus Aspergillus nomius

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the A. nomius type strain was sequenced using a personal genome machine. Annotation of the genes was undertaken, followed by gene ontology and an investigation into the number of secondary metabolite clusters. Comparative studies with other Aspergillus species involved shared/unique ge...

  11. Use of Whole Genome Sequence Data To Infer Baculovirus Phylogeny

    PubMed Central

    Herniou, Elisabeth A.; Luque, Teresa; Chen, Xinwen; Vlak, Just M.; Winstanley, Doreen; Cory, Jennifer S.; O'Reilly, David R.

    2001-01-01

    Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses. PMID:11483757

  12. Genomic distribution of simple sequence repeats in Brassica rapa.

    PubMed

    Hong, Chang Pyo; Piao, Zhong Yun; Kang, Tae Wook; Batley, Jacqueline; Yang, Tae-Jin; Hur, Yoon-Kang; Bhak, Jong; Park, Beom-Seok; Edwards, David; Lim, Yong Pyo

    2007-06-30

    Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa. PMID:17646709

  13. Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences

    PubMed Central

    Chen, Leslie Y.Y.; Lu, Szu-Hsien; Shih, Edward S.C.; Hwang, Ming-Jing

    2002-01-01

    As more and more genomic DNAs are sequenced to characterize human genetic variations, the demand for a very fast and accurate method to genomically position these DNA sequences is high. We have developed a new mapping method that does not require sequence alignment. In this method, we first identified DNA fragments of 15 bp in length that are unique in the human genome and then used them to position single nucleotide polymorphism (SNP) sequences. By use of four desktop personal computers with AMD K7 (1 GHz) processors, our new method mapped more than 1.6 million SNP sequences in 20 hr and achieved a very good agreement with mapping results from alignment-based methods. PMID:12097348

  14. Genome sequence of the date palm Phoenix dactylifera L

    PubMed Central

    Al-Mssallem, Ibrahim S.; Hu, Songnian; Zhang, Xiaowei; Lin, Qiang; Liu, Wanfei; Tan, Jun; Yu, Xiaoguang; Liu, Jiucheng; Pan, Linlin; Zhang, Tongwu; Yin, Yuxin; Xin, Chengqi; Wu, Hao; Zhang, Guangyu; Ba Abdullah, Mohammed M.; Huang, Dawei; Fang, Yongjun; Alnakhli, Yasser O.; Jia, Shangang; Yin, An; Alhuzimi, Eman M.; Alsaihati, Burair A.; Al-Owayyed, Saad A.; Zhao, Duojun; Zhang, Sun; Al-Otaibi, Noha A.; Sun, Gaoyuan; Majrashi, Majed A.; Li, Fusen; Tala; Wang, Jixiang; Yun, Quanzheng; Alnassar, Nafla A.; Wang, Lei; Yang, Meng; Al-Jelaify, Rasha F.; Liu, Kan; Gao, Shenghan; Chen, Kaifu; Alkhaldi, Samiyah R.; Liu, Guiming; Zhang, Meng; Guo, Haiyan; Yu, Jun

    2013-01-01

    Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm’s unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants. PMID:23917264

  15. Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis

    PubMed Central

    Sato, Kengo; Kuroki, Yoko; Kumita, Wakako; Fujiyama, Asao; Toyoda, Atsushi; Kawai, Jun; Iriki, Atsushi; Sasaki, Erika; Okano, Hideyuki; Sakakibara, Yasubumi

    2015-01-01

    The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis Consortium. The draft was based on whole-genome shotgun sequencing, and the current assembly version is Callithrix_jacches-3.2.1, but there still exist 187,214 undetermined gap regions and supercontigs and relatively short contigs that are unmapped to chromosomes in the draft genome. We performed resequencing and assembly of the genome of common marmoset by deep sequencing with high-throughput sequencing technology. Several different sequence runs using Illumina sequencing platforms were executed, and 181 Gbp of high-quality bases including mate-pairs with long insert lengths of 3, 8, 20, and 40 Kbp were obtained, that is, approximately 60× coverage. The resequencing significantly improved the MGSAC draft genome sequence. The N50 of the contigs, which is a statistical measure used to evaluate assembly quality, doubled. As a result, 51% of the contigs (total length: 299 Mbp) that were unmapped to chromosomes in the MGSAC draft were merged with chromosomal contigs, and the improved genome sequence helped to detect 5,288 new genes that are homologous to human cDNAs and the gaps in 5,187 transcripts of the Ensembl gene annotations were completely filled. PMID:26586576

  16. Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

    PubMed Central

    2010-01-01

    Background Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. Results Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89%) and that in the Te. nigroviridis genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp). Conclusion Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non

  17. Complete genome sequence of Ferroglobus placidus AEDII12DO

    SciTech Connect

    Anderson, Iain; Risso, Carla; Holmes, Dawn; Lucas, Susan; Copeland, A; Lapidus, Alla L.; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Saunders, Elizabeth H; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Larimer, Frank W; Land, Miriam L; Hauser, Loren John; Woyke, Tanja; Lovley, Derek; Kyrpides, Nikos C; Ivanova, N

    2011-01-01

    Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryar- chaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemoli- thoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and anno- tation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was se- quenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.

  18. Complete genome sequence of Serratia plymuthica strain AS12

    SciTech Connect

    Neupane, Saraswoti; Finlay, Roger D.; Alstrom, Sadhna; Goodwin, Lynne A.; Kyrpides, Nikos C; Lucas, Susan; Lapidus, Alla L.; Bruce, David; Pitluck, Sam; Peters, Lin; Ovchinnikova, Galina; Chertkov, Olga; Han, James; Han, Cliff; Tapia, Roxanne; Detter, J. Chris; Land, Miriam L; Hauser, Loren John; Cheng, Jan-Fang; Ivanova, N; Pagani, Ioanna; Klenk, Hans-Peter; Woyke, Tanja; Hogberg, Nils

    2012-01-01

    A plant associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest due to its plant growth promoting and plant pathogen inhibiting ability. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled 'Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens'.

  19. Complete mitochondrial genome sequence of Aoluguya reindeer (Rangifer tarandus).

    PubMed

    Ju, Yan; Liu, Huamiao; Rong, Min; Yang, Yifeng; Wei, Haijun; Shao, Yuanchen; Chen, Xiumin; Xing, Xiumei

    2016-05-01

    The complete mitochondria genome of the reindeer, Rangifer tarandus, was determined by accurate polymerase chain reaction. The entire genome is 16,357 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a D-loop region, all of which are arranged in a typical vertebrate manner. The overall base composition of the reindeer's mitochondrial genome is 33.7% of A, 23.1% of C, 30.1% of T and 13.2%of G. A termination associated sequence and several conserved central sequence block domains were discovered within the control region. PMID:25469816

  20. Complete genome sequence of Serratia plymuthica strain AS12

    PubMed Central

    Finlay, Roger D.; Alström, Sadhna; Goodwin, Lynne; Kyrpides, Nikos C.; Lucas, Susan; Lapidus, Alla; Bruce, David; Pitluck, Sam; Peters, Lin; Ovchinnikova, Galina; Chertkov, Olga; Han, James; Han, Cliff; Tapia, Roxanne; Detter, John C.; Land, Miriam; Hauser, Loren; Cheng, Jan-Fang; Ivanova, Natalia; Pagani, Ioanna; Klenk, Hans-Peter; Woyke, Tanja; Högberg, Nils

    2012-01-01

    A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled “Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens”. PMID:22768360

  1. Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions

    PubMed Central

    Druet, T; Macleod, I M; Hayes, B J

    2014-01-01

    Genomic prediction from whole-genome sequence data is attractive, as the accuracy of genomic prediction is no longer bounded by extent of linkage disequilibrium between DNA markers and causal mutations affecting the trait, given the causal mutations are in the data set. A cost-effective strategy could be to sequence a small proportion of the population, and impute sequence data to the rest of the reference population. Here, we describe strategies for selecting individuals for sequencing, based on either pedigree relationships or haplotype diversity. Performance of these strategies (number of variants detected and accuracy of imputation) were evaluated in sequence data simulated through a real Belgian Blue cattle pedigree. A strategy (AHAP), which selected a subset of individuals for sequencing that maximized the number of unique haplotypes (from single-nucleotide polymorphism panel data) sequenced gave good performance across a range of variant minor allele frequencies. We then investigated the optimum number of individuals to sequence by fold coverage given a maximum total sequencing effort. At 600 total fold coverage (x 600), the optimum strategy was to sequence 75 individuals at eightfold coverage. Finally, we investigated the accuracy of genomic predictions that could be achieved. The advantage of using imputed sequence data compared with dense SNP array genotypes was highly dependent on the allele frequency spectrum of the causative mutations affecting the trait. When this followed a neutral distribution, the advantage of the imputed sequence data was small; however, when the causal mutations all had low minor allele frequencies, using the sequence data improved the accuracy of genomic prediction by up to 30%. PMID:23549338

  2. Biased distribution of DNA uptake sequences towards genome maintenance genes.

    PubMed

    Davidsen, Tonje; Rødland, Einar A; Lagesen, Karin; Seeberg, Erling; Rognes, Torbjørn; Tønjum, Tone

    2004-01-01

    Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat genomic sequences in the human pathogens Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae and found that by far the most frequent 9-10mers residing within coding regions are the DNA uptake sequences (DUS) required for natural genetic transformation. More importantly, we found a significantly higher density of DUS within genes involved in DNA repair, recombination, restriction-modification and replication than in any other annotated gene group in these organisms. Pasteurella multocida also displayed high frequencies of a putative DUS identical to that previously identified in H.influenzae and with a skewed distribution towards genome maintenance genes, indicating that this bacterium might be transformation competent under certain conditions. These results imply that the high frequency of DUS in genome maintenance genes is conserved among phylogenetically divergent species and thus are of significant biological importance. Increased DUS density is expected to enhance DNA uptake and the over-representation of DUS in genome maintenance genes might reflect facilitated recovery of genome preserving functions. For example, transient and beneficial increase in genome instability can be allowed during pathogenesis simply through loss of antimutator genes, since these DUS-containing sequences will be preferentially recovered. Furthermore, uptake of such genes could provide a mechanism for facilitated recovery from DNA damage after genotoxic stress. PMID:14960717

  3. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    SciTech Connect

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  4. Sequencing and comparative analyses of the genomes of zoysiagrasses.

    PubMed

    Tanaka, Hidenori; Hirakawa, Hideki; Kosugi, Shunichi; Nakayama, Shinobu; Ono, Akiko; Watanabe, Akiko; Hashiguchi, Masatsugu; Gondo, Takahiro; Ishigaki, Genki; Muguerza, Melody; Shimizu, Katsuya; Sawamura, Noriko; Inoue, Takayasu; Shigeki, Yuichi; Ohno, Naoki; Tabata, Satoshi; Akashi, Ryo; Sato, Shusei

    2016-04-01

    Zoysiais a warm-season turfgrass, which comprises 11 allotetraploid species (2n= 4x= 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession 'Nagirizaki' (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella 'Wakaba' and Z. pacifica 'Zanpa' were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica'Kyoto', Z. japonica'Miyagi' and Z. matrella'Chiba Fair Green', were accumulated, and aligned against the reference genome of 'Nagirizaki' along with those from 'Wakaba' and 'Zanpa'. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the 'Zoysia Genome Database' at http://zoysia.kazusa.or.jp. PMID:26975196

  5. Sequencing and comparative analyses of the genomes of zoysiagrasses

    PubMed Central

    Tanaka, Hidenori; Hirakawa, Hideki; Kosugi, Shunichi; Nakayama, Shinobu; Ono, Akiko; Watanabe, Akiko; Hashiguchi, Masatsugu; Gondo, Takahiro; Ishigaki, Genki; Muguerza, Melody; Shimizu, Katsuya; Sawamura, Noriko; Inoue, Takayasu; Shigeki, Yuichi; Ohno, Naoki; Tabata, Satoshi; Akashi, Ryo; Sato, Shusei

    2016-01-01

    Zoysia is a warm-season turfgrass, which comprises 11 allotetraploid species (2n = 4x = 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession ‘Nagirizaki’ (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella ‘Wakaba’ and Z. pacifica ‘Zanpa’ were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica ‘Kyoto’, Z. japonica ‘Miyagi’ and Z. matrella ‘Chiba Fair Green’, were accumulated, and aligned against the reference genome of ‘Nagirizaki’ along with those from ‘Wakaba’ and ‘Zanpa’. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the ‘Zoysia Genome Database’ at http://zoysia.kazusa.or.jp. PMID:26975196

  6. Comparison of mitochondrial genome sequences of pangolins (Mammalia, Pholidota).

    PubMed

    Hassanin, Alexandre; Hugot, Jean-Pierre; van Vuuren, Bettine Jansen

    2015-04-01

    The complete mitochondrial genome was sequenced for three species of pangolins, Manis javanica, Phataginus tricuspis, and Smutsia temminckii, and comparisons were made with two other species, Manis pentadactyla and Phataginus tetradactyla. The genome of Manidae contains the 37 genes found in a typical mammalian genome, and the structure of the control region is highly conserved among species. In Manis, the overall base composition differs from that found in African genera. Phylogenetic analyses support the monophyly of the genera Manis, Phataginus, and Smutsia, as well as the basal division between Maninae and Smutsiinae. Comparisons with GenBank sequences reveal that the reference genomes of M. pentadactyla and P. tetradactyla (accession numbers NC_016008 and NC_004027) were sequenced from misidentified taxa, and that a new species of tree pangolin should be described in Gabon. PMID:25746396

  7. Draft genome sequence of adzuki bean, Vigna angularis.

    PubMed

    Kang, Yang Jae; Satyawan, Dani; Shim, Sangrea; Lee, Taeyoung; Lee, Jayern; Hwang, Won Joo; Kim, Sue K; Lestari, Puji; Laosatit, Kularb; Kim, Kil Hyun; Ha, Tae Joung; Chitikineni, Annapurna; Kim, Moon Young; Ko, Jong-Min; Gwag, Jae-Gyun; Moon, Jung-Kyung; Lee, Yeong-Ho; Park, Beom-Seok; Varshney, Rajeev K; Lee, Suk-Ha

    2015-01-01

    Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis, and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean. PMID:25626881

  8. Long-read sequence assembly of the gorilla genome.

    PubMed

    Gordon, David; Huddleston, John; Chaisson, Mark J P; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, LaDeana W; Dunn, Christopher; Baker, Carl; Armstrong, Joel; Diekhans, Mark; Paten, Benedict; Shendure, Jay; Wilson, Richard K; Haussler, David; Chin, Chen-Shan; Eichler, Evan E

    2016-04-01

    Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome. PMID:27034376

  9. The complete chloroplast genome sequence of Dieffenbachia seguine (Araceae).

    PubMed

    Wang, Bin; Han, Limin; Chen, Chen; Wang, Zhezhi

    2016-07-01

    The nucleotide sequence of the chloroplast genome from Dieffenbachia seguine is the first to have complete genome sequence from genus of Dieffenbachia family Araceae. The genome size is 163 699 bp in length, with 36.4% GC content. A pair of inverted repeats (IRs, 25 235 bp) is separated by a large single copy region (LSC, 90 780 bp) and a small single copy region (SSC, 22 449 bp). The chloroplast genome contains 113 unique genes, 88 protein-coding genes, 37 tRNA genes, and four rRNA genes. In these genes, 16 genes contained single intron and two genes composed of double introns. A maximum likelihood phylogenetic analysis using complete chloroplast genome revealed that Dieffenbachia seguine belongs to the Araceae family of the Arecidae group, which is conform to the traditional classification. PMID:26153749

  10. Draft Genome Sequence of Aeromonas sp. Strain EERV15.

    PubMed

    Ehsani, Elham; Barrantes, Israel; Vandermaesen, Johanna; Geffers, Robert; Jarek, Michael; Boon, Nico; Springael, Dirk; Pieper, Dietmar H; Vilchez-Vargas, Ramiro

    2016-01-01

    We report here the draft genome sequence of Aeromonas sp. strain EERV15 isolated from sand filter. The organism most closely related to Aeromonas sp. EERV15 is Aeromonas veronii B565, with an average 83% amino acid sequence similarity of putatively encoded protein open reading frames. PMID:27540061

  11. Complete Genome Sequence of the Alfalfa latent virus.

    PubMed

    Nemchinov, Lev G; Shao, Jonathan; Postnikova, Olga A

    2015-01-01

    The first complete genome sequence of the Alfalfa latent carlavirus (ALV) was obtained by primer walking and Illumina RNA sequencing. The virus differs substantially from the Czech ALV isolate and the Pea streak virus isolate from Wisconsin. The absence of a clear nucleic acid-binding protein indicates ALV divergence from other carlaviruses. PMID:25883281

  12. Draft Genome Sequence of Biocontrol Agent Bacillus cereus UW85

    PubMed Central

    Lozano, Gabriel L.; Holt, Jonathan; Rasko, David A.; Thomas, Michael G.

    2016-01-01

    Bacillus cereus UW85 was isolated from a root of a field-grown alfalfa plant from Arlington, WI, and identified for its ability to suppress damping off, a disease caused by Phytophthora megasperma f. sp. medicaginis on alfalfa. Here, we report the draft genome sequence of B. cereus UW85, obtained by a combination of Sanger and Illumina sequencing. PMID:27587823

  13. Genome Sequence of a Mycoplasma meleagridis Field Strain.

    PubMed

    Rocha, Ticiana S; Bertolotti, Luigi; Catania, Salvatore; Pourquier, Philippe; Rosati, Sergio

    2016-01-01

    Mycoplasma meleagridis is a major cause of disease and economic loss in turkeys. Here, we report the genome sequence of an M. meleagridis field strain, which enlarges the knowledge about this bacterium and helps the identification of possible coding sequences for drug resistance genes and specific antigens. PMID:26941131

  14. Draft Genome Sequence of Aeromonas sp. Strain EERV15

    PubMed Central

    Ehsani, Elham; Barrantes, Israel; Vandermaesen, Johanna; Geffers, Robert; Jarek, Michael; Boon, Nico; Springael, Dirk; Pieper, Dietmar H.

    2016-01-01

    We report here the draft genome sequence of Aeromonas sp. strain EERV15 isolated from sand filter. The organism most closely related to Aeromonas sp. EERV15 is Aeromonas veronii B565, with an average 83% amino acid sequence similarity of putatively encoded protein open reading frames. PMID:27540061

  15. Complete Genome Sequence of Caulobacter crescentus Siphophage Sansa

    PubMed Central

    Vara, Leonardo; Kane, Ashley A.; Cahill, Jesse L.; Rasche, Eric S.

    2015-01-01

    Caulobacter crescentus is a Gram-negative dimorphic model organism used to study cell differentiation. Siphophage Sansa is a newly isolated siphophage with an icosahedral capsid that infects C. crescentus. Sansa shares no sequence similarity to other phages deposited in GenBank. Here, we describe its genome sequence and general features. PMID:26450723

  16. Complete Genome Sequence of Caulobacter crescentus Siphophage Sansa.

    PubMed

    Vara, Leonardo; Kane, Ashley A; Cahill, Jesse L; Rasche, Eric S; Kuty Everett, Gabriel F

    2015-01-01

    Caulobacter crescentus is a Gram-negative dimorphic model organism used to study cell differentiation. Siphophage Sansa is a newly isolated siphophage with an icosahedral capsid that infects C. crescentus. Sansa shares no sequence similarity to other phages deposited in GenBank. Here, we describe its genome sequence and general features. PMID:26450723

  17. Complete Genome Sequence of Vibrio alginolyticus ZJ-T.

    PubMed

    Deng, Yiqin; Chen, Chang; Zhao, Zhe; Huang, Xiaochun; Yang, Yiying; Ding, Xiongqi

    2016-01-01

    Vibrio alginolyticus is a ubiquitous Gram-negative bacterium which is normally distributed in the coastal and estuarine environments. It has been suggested to be an opportunistic pathogen to both marine animals and humans, Here, the completed genome sequence of V. alginolyticus ZJ-T was determined by Illumina high-throughput sequencing. PMID:27587824

  18. Complete Genome Sequence of Vibrio alginolyticus ZJ-T

    PubMed Central

    Deng, Yiqin; Zhao, Zhe; Huang, Xiaochun; Yang, Yiying; Ding, Xiongqi

    2016-01-01

    Vibrio alginolyticus is a ubiquitous Gram-negative bacterium which is normally distributed in the coastal and estuarine environments. It has been suggested to be an opportunistic pathogen to both marine animals and humans, Here, the completed genome sequence of V. alginolyticus ZJ-T was determined by Illumina high-throughput sequencing. PMID:27587824

  19. GENOMIC SEQUENCE ANALYSIS OF LEPTOSPIRA BORGPETERSENII SEROVAR HARDJO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genomic library from Leptospira borgpetersenii serovar hardjo strain JB197 was prepared by mechanically shearing the DNA and inserting it into a positive selection vector. DNA was prepared from approximately 22,000 random clones and used as templates for automated sequencing. Sequence data was c...

  20. Complete Genome Sequence of the Alfalfa latent virus

    PubMed Central

    Shao, Jonathan; Postnikova, Olga A.

    2015-01-01

    The first complete genome sequence of the Alfalfa latent carlavirus (ALV) was obtained by primer walking and Illumina RNA sequencing. The virus differs substantially from the Czech ALV isolate and the Pea streak virus isolate from Wisconsin. The absence of a clear nucleic acid-binding protein indicates ALV divergence from other carlaviruses. PMID:25883281

  1. Genome sequence of Stachybotrys chartarum Strain 51-11

    EPA Science Inventory

    Stachybotrys chartarum strain 51-11 genome was sequenced by shotgun sequencing utilizing Illumina Hiseq 2000 and PacBio long read technology. Since Stachybotrys chartarum has been implicated in health impacts within water-damaged buildings, any information extracted from the geno...

  2. Genome Sequence of a Mycoplasma meleagridis Field Strain

    PubMed Central

    Bertolotti, Luigi; Catania, Salvatore; Pourquier, Philippe; Rosati, Sergio

    2016-01-01

    Mycoplasma meleagridis is a major cause of disease and economic loss in turkeys. Here, we report the genome sequence of an M. meleagridis field strain, which enlarges the knowledge about this bacterium and helps the identification of possible coding sequences for drug resistance genes and specific antigens. PMID:26941131

  3. Draft Genome Sequence of Biocontrol Agent Bacillus cereus UW85.

    PubMed

    Lozano, Gabriel L; Holt, Jonathan; Ravel, Jacques; Rasko, David A; Thomas, Michael G; Handelsman, Jo

    2016-01-01

    Bacillus cereus UW85 was isolated from a root of a field-grown alfalfa plant from Arlington, WI, and identified for its ability to suppress damping off, a disease caused by Phytophthora megasperma f. sp. medicaginis on alfalfa. Here, we report the draft genome sequence of B. cereus UW85, obtained by a combination of Sanger and Illumina sequencing. PMID:27587823

  4. Draft Genome Sequence of Type Strain Streptococcus gordonii ATCC 10558

    PubMed Central

    Rasmussen, Louise H.; Dargis, Rimtas; Skovgaard, Ole

    2016-01-01

    Streptococcus gordonii ATCC 10558T was isolated from a patient with infective endocarditis in 1946 and announced as a type strain in 1989. Here, we report the 2,154,510-bp draft genome sequence of S. gordonii ATCC 10558T. This sequence will contribute to knowledge about the pathogenesis of infective endocarditis. PMID:26893427

  5. Genome Sequence of Lactobacillus plantarum Strain UCMA 3037

    PubMed Central

    Naz, Saima; Tareb, Raouf; Bernardeau, Marion; Vaisse, Melissa; Lucchetti-Miganeh, Celine; Rechenmann, Mathias

    2013-01-01

    Nucleic acid of the strain Lactobacillus plantarum UCMA 3037, isolated from raw milk camembert cheese in our laboratory, was sequenced. We present its draft genome sequence with the aim of studying its functional properties and relationship to the cheese ecosystem. PMID:23704179

  6. Genome Sequence of Lactobacillus plantarum Strain UCMA 3037.

    PubMed

    Naz, Saima; Tareb, Raouf; Bernardeau, Marion; Vaisse, Melissa; Lucchetti-Miganeh, Celine; Rechenmann, Mathias; Vernoux, Jean-Paul

    2013-01-01

    Nucleic acid of the strain Lactobacillus plantarum UCMA 3037, isolated from raw milk camembert cheese in our laboratory, was sequenced. We present its draft genome sequence with the aim of studying its functional properties and relationship to the cheese ecosystem. PMID:23704179

  7. Genome Sequences of Five Nonvirulent Listeria monocytogenes Serovar 4 Strains

    PubMed Central

    Shen, Yang; Loessner, Martin J.

    2016-01-01

    We present the complete genome sequences of five nonpathogenic Listeria monocytogenes serovar 4 strains: WSLC 1018 (4e), 1019 (4c), 1020 (4a), 1033 (4d), and 1047 (4d). These sequences may help to uncover genes involved in the synthesis of the serovar antigens—phenotypic determinants of virulence deemed clinically relevant. PMID:27034489

  8. Sequencing the Genome of the Heirloom Watermelon Cultivar Charleston Gray

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the watermelon cultivar Charleston Gray, a major heirloom which has been used in breeding programs of many watermelon cultivars, was sequenced. Our strategy involved a hybrid approach using the Illumina and 454/Titanium next-generation sequencing technologies. For Illumina, shotgun g...

  9. Corruption of genomic databases with anomalous sequence.

    PubMed Central

    Lamperti, E D; Kittelberger, J M; Smith, T F; Villa-Komaroff, L

    1992-01-01

    We describe evidence that DNA sequences from vectors used for cloning and sequencing have been incorporated accidentally into eukaryotic entries in the GenBank database. These incorporations were not restricted to one type of vector or to a single mechanism. Many minor instances may have been the result of simple editing errors, but some entries contained large blocks of vector sequence that had been incorporated by contamination or other accidents during cloning. Some cases involved unusual rearrangements and areas of vector distant from the normal insertion sites. Matches to vector were found in 0.23% of 20,000 sequences analyzed in GenBank Release 63. Although the possibility of anomalous sequence incorporation has been recognized since the inception of GenBank and should be easy to avoid, recent evidence suggests that this problem is increasing more quickly than the database itself. The presence of anomalous sequence may have serious consequences for the interpretation and use of database entries, and will have an impact on issues of database management. The incorporated vector fragments described here may also be useful for a crude estimate of the fidelity of sequence information in the database. In alignments with well-defined ends, the matching sequences showed 96.8% identity to vector; when poorer matches with arbitrary limits were included, the aggregate identity to vector sequence was 94.8%. PMID:1614861

  10. Genomic Sequencing of Single Microbial Cells from Environmental Samples

    SciTech Connect

    Ishoey, Thomas; Woyke, Tanja; Stepanauskas, Ramunas; Novotny, Mark; Lasken, Roger S.

    2008-02-01

    Recently developed techniques allow genomic DNA sequencing from single microbial cells [Lasken RS: Single-cell genomic sequencing using multiple displacement amplification, Curr Opin Microbiol 2007, 10:510-516]. Here, we focus on research strategies for putting these methods into practice in the laboratory setting. An immediate consequence of single-cell sequencing is that it provides an alternative to culturing organisms as a prerequisite for genomic sequencing. The microgram amounts of DNA required as template are amplified from a single bacterium by a method called multiple displacement amplification (MDA) avoiding the need to grow cells. The ability to sequence DNA from individual cells will likely have an immense impact on microbiology considering the vast numbers of novel organisms, which have been inaccessible unless culture-independent methods could be used. However, special approaches have been necessary to work with amplified DNA. MDA may not recover the entire genome from the single copy present in most bacteria. Also, some sequence rearrangements can occur during the DNA amplification reaction. Over the past two years many research groups have begun to use MDA, and some practical approaches to single-cell sequencing have been developed. We review the consensus that is emerging on optimum methods, reliability of amplified template, and the proper interpretation of 'composite' genomes which result from the necessity of combining data from several single-cell MDA reactions in order to complete the assembly. Preferred laboratory methods are considered on the basis of experience at several large sequencing centers where >70% of genomes are now often recovered from single cells. Methods are reviewed for preparation of bacterial fractions from environmental samples, single-cell isolation, DNA amplification by MDA, and DNA sequencing.

  11. Modeling genome coverage in single-cell sequencing

    PubMed Central

    Daley, Timothy; Smith, Andrew D.

    2014-01-01

    Motivation: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material. Results: We propose a method to predict the genome coverage of a deep sequencing experiment using information from an initial shallow sequencing experiment mapped to a reference genome. The observed coverage statistics are used in a non-parametric empirical Bayes Poisson model to estimate the gain in coverage from deeper sequencing. This approach allows researchers to know statistical features of deep sequencing experiments without actually sequencing deeply, providing a basis for optimizing and comparing single-cell sequencing protocols or screening libraries. Availability and implementation: The method is available as part of the preseq software package. Source code is available at http://smithlabresearch.org/preseq. Contact: andrewds@usc.edu Supplementary information: Supplementary material is available at Bioinformatics online. PMID:25107873

  12. Complete genome sequence of southern tomato virus identified from China using next generation sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequence of a double-stranded RNA (dsRNA) virus, southern tomato virus (STV), on tomatoes in China, was elucidated using small RNAs deep sequencing. The identified STV_CN12 shares 99% sequence identity to other isolates from Mexico, France, Spain, and U.S. This is the first report ...

  13. Draft Genome Sequence of Neisseria gonorrhoeae Sequence Type 1407, a Multidrug-Resistant Clinical Isolate.

    PubMed

    Anselmo, A; Ciammaruconi, A; Carannante, A; Neri, A; Fazio, C; Fortunato, A; Palozzi, A M; Vacca, P; Fillo, S; Lista, F; Stefanelli, P

    2015-01-01

    Gonorrhea may become untreatable due to the spread of resistant or multidrug-resistant strains. Cefixime-resistant gonococci belonging to sequence type 1407 have been described worldwide. We report the genome sequence of Neisseria gonorrhoeae strain G2891, a multidrug-resistant isolate of sequence type 1407, collected in Italy in 2013. PMID:26272575

  14. Widespread mitovirus sequences in plant genomes

    PubMed Central

    Warner, Benjamin E.; Yerramsetty, Pradeep

    2015-01-01

    The exploration of the evolution of RNA viruses has been aided recently by the discovery of copies of fragments or complete genomes of non-retroviral RNA viruses (Non-retroviral Endogenous RNA Viral Elements, or NERVEs) in many eukaryotic nuclear genomes. Among the most prominent NERVEs are partial copies of the RNA dependent RNA polymerase (RdRP) of the mitoviruses in plant mitochondrial genomes. Mitoviruses are in the family Narnaviridae, which are the simplest viruses, encoding only a single protein (the RdRP) in their unencapsidated viral plus strand. Narnaviruses are known only in fungi, and the origin of plant mitochondrial mitovirus NERVEs appears to be horizontal transfer from plant pathogenic fungi. At least one mitochondrial mitovirus NERVE, but not its nuclear copy, is expressed. PMID:25870770

  15. Initial sequence and comparative analysis of the cat genome

    PubMed Central

    Pontius, Joan U.; Mullikin, James C.; Smith, Douglas R.; Lindblad-Toh, Kerstin; Gnerre, Sante; Clamp, Michele; Chang, Jean; Stephens, Robert; Neelam, Beena; Volfovsky, Natalia; Schäffer, Alejandro A.; Agarwala, Richa; Narfström, Kristina; Murphy, William J.; Giger, Urs; Roca, Alfred L.; Antunes, Agostinho; Menotti-Raymond, Marilyn; Yuhki, Naoya; Pecon-Slattery, Jill; Johnson, Warren E.; Bourque, Guillaume; Tesler, Glenn; O’Brien, Stephen J.

    2007-01-01

    The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence. PMID:17975172

  16. Sequence Analysis of the Genome of Carnation (Dianthus caryophyllus L.)

    PubMed Central

    Yagi, Masafumi; Kosugi, Shunichi; Hirakawa, Hideki; Ohmiya, Akemi; Tanase, Koji; Harada, Taro; Kishimoto, Kyutaro; Nakayama, Masayoshi; Ichimura, Kazuo; Onozaki, Takashi; Yamaguchi, Hiroyasu; Sasaki, Nobuhiro; Miyahara, Taira; Nishizaki, Yuzo; Ozeki, Yoshihiro; Nakamura, Noriko; Suzuki, Takamasa; Tanaka, Yoshikazu; Sato, Shusei; Shirasawa, Kenta; Isobe, Sachiko; Miyamura, Yoshinori; Watanabe, Akiko; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Tabata, Satoshi

    2014-01-01

    The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. ‘Francesco’ was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568 887 315 bp, consisting of 45 088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16 644 bp and 60 737 bp, respectively, and the longest scaffold was 1 287 144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp. PMID:24344172

  17. Complete genome sequence of Treponema pallidum, the syphilis spirochete.

    PubMed

    Fraser, C M; Norris, S J; Weinstock, G M; White, O; Sutton, G G; Dodson, R; Gwinn, M; Hickey, E K; Clayton, R; Ketchum, K A; Sodergren, E; Hardham, J M; McLeod, M P; Salzberg, S; Peterson, J; Khalak, H; Richardson, D; Howell, J K; Chidambaram, M; Utterback, T; McDonald, L; Artiach, P; Bowman, C; Cotton, M D; Fujii, C; Garland, S; Hatch, B; Horst, K; Roberts, K; Sandusky, M; Weidman, J; Smith, H O; Venter, J C

    1998-07-17

    The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes. PMID:9665876

  18. The genome sequence of four isolates from the family Lichtheimiaceae

    PubMed Central

    Chibucos, Marcus C.; Etienne, Kizee A.; Orvis, Joshua; Lee, Hongkyu; Daugherty, Sean; Lockhart, Shawn R.; Ibrahim, Ashraf S.; Bruno, Vincent M.

    2015-01-01

    This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intraspecies and interspecies genetic variation within the Mucoraceae family of pathogenic fungi. PMID:25857734

  19. Genome sequencing of a single tardigrade Hypsibius dujardini individual

    PubMed Central

    Arakawa, Kazuharu; Yoshida, Yuki; Tomita, Masaru

    2016-01-01

    Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies. PMID:27529330

  20. Genome sequencing of a single tardigrade Hypsibius dujardini individual.

    PubMed

    Arakawa, Kazuharu; Yoshida, Yuki; Tomita, Masaru

    2016-01-01

    Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies. PMID:27529330

  1. A physical map of the papaya genome with integrated genetic map and genome sequence

    PubMed Central

    2009-01-01

    Background Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly. Results The physical map consists of 963 contigs, representing 9.4× genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes. Conclusion A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly

  2. Genome sequence and comparative genome analysis of Pseudomonas syringae pv. syringae type strain ATCC 19310.

    PubMed

    Park, Yong-Soon; Jeong, Haeyoung; Sim, Young Mi; Yi, Hwe-Su; Ryu, Choong-Min

    2014-04-01

    Pseudomonas syringae pv. syringae (Psy) is a major bacterial pathogen of many economically important plant species. Despite the severity of its impact, the genome sequence of the type strain has not been reported. Here, we present the draft genome sequence of Psy ATCC 19310. Comparative genomic analysis revealed that Psy ATCC 19310 is closely related to Psy B728a. However, only a few type III effectors, which are key virulence factors, are shared by the two strains, indicating the possibility of host-pathogen specificity and genome dynamics, even under the pathovar level. PMID:24444998

  3. Identification of genes in genomic and EST sequences

    SciTech Connect

    Fields, C.; Adams, M.D.; Kerlavage, A.R.; Dubnick, M.; McCombie, W.R.; Martin-Gallardo, A.; Venter, J.C.; White, O.

    1993-12-31

    Currently-available software tools are capable of predicting the locations of most protein-coding genes in anonymous genomic DNA sequences. The use of predicted exxon to select primers for PCR amplification from cDNA libraries allows the complete structures of novel genes to be determined efficiently. As the number of expressed sequence tag (EST) sequences increases, the fraction of genes that can be localized in genomic sequences by searching EST databases will rapidly approach unity. The challenge for automated DNA sequence analysis is now to develop methods for accurately predicting gene structure and alternative splicing patterns. Substantially improving current accuracies in gene structure prediction will require retrospective comparative analysis of sequences from different organisms and gene families.

  4. Legume genomics: understanding biology through DNA and RNA sequencing

    PubMed Central

    O'Rourke, Jamie A.; Bolon, Yung-Tsi; Bucciarelli, Bruna; Vance, Carroll P.

    2014-01-01

    Background The legume family (Leguminosae) consists of approx. 17 000 species. A few of these species, including, but not limited to, Phaseolus vulgaris, Cicer arietinum and Cajanus cajan, are important dietary components, providing protein for approx. 300 million people worldwide. Additional species, including soybean (Glycine max) and alfalfa (Medicago sativa), are important crops utilized mainly in animal feed. In addition, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30 % of available nitrogen for the next season of crops. The application of high-throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture and domestication. Scope and Conclusions This review presents an overview of the current state of legume genomics and explores the role that next-generation sequencing technologies play in advancing legume genomics. The adoption of next-generation sequencing and implementation of associated bioinformatic tools has allowed researchers to turn each species of interest into their own model organism. To illustrate the power of next-generation sequencing, an in-depth overview of the transcriptomes of both soybean and white lupin (Lupinus albus) is provided. The soybean transcriptome focuses on analysing seed development in two near-isogenic lines, examining the role of transporters, oil biosynthesis and nitrogen utilization. The white lupin transcriptome analysis examines how phosphate deficiency alters gene expression patterns, inducing the formation of cluster roots. Such studies illustrate the power of next-generation sequencing and bioinformatic analyses in elucidating the gene networks underlying biological processes. PMID:24769535

  5. Spectral entropy criteria for structural segmentation in genomic DNA sequences

    NASA Astrophysics Data System (ADS)

    Chechetkin, V. R.; Lobzin, V. V.

    2004-07-01

    The spectral entropy is calculated with Fourier structure factors and characterizes the level of structural ordering in a sequence of symbols. It may efficiently be applied to the assessment and reconstruction of the modular structure in genomic DNA sequences. We present the relevant spectral entropy criteria for the local and non-local structural segmentation in DNA sequences. The results are illustrated with the model examples and analysis of intervening exon-intron segments in the protein-coding regions.

  6. Ion Torrent Personal Genome Machine Sequencing for Genomic Typing of Neisseria meningitidis for Rapid Determination of Multiple Layers of Typing Information

    PubMed Central

    Szczepanowski, Rafael; Claus, Heike; Jünemann, Sebastian; Prior, Karola; Harmsen, Dag

    2012-01-01

    Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring. PMID:22461678

  7. Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine.

    PubMed

    Granberg, F; Bálint, Á; Belák, S

    2016-04-01

    Next-generation sequencing (NGS), also referred to as deep, high-throughput or massively parallel sequencing, is a powerful new tool that can be used for the complex diagnosis and intensive monitoring of infectious disease in veterinary medicine. NGS technologies are also being increasingly used to study the aetiology, genomics, evolution and epidemiology of infectious disease, as well as host-pathogen interactions and other aspects of infection biology. This review briefly summarises recent progress and achievements in this field by first introducing a range of novel techniques and then presenting examples of NGS applications in veterinary infection biology. Various work steps and processes for sampling and sample preparation, sequence analysis and comparative genomics, and improving the accuracy of genomic prediction are discussed, as are bioinformatics requirements. Examples of sequencing-based applications and comparative genomics in veterinary medicine are then provided. This review is based on novel references selected from the literature and on experiences of the World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden. PMID:27217166

  8. Living laboratory: Whole-genome sequencing as a learning healthcare enterprise

    PubMed Central

    Angrist, M.; Jamal, L.

    2014-01-01

    With the proliferation of affordable large-scale human genomic data come profound and vexing questions about management of such data and their clinical uncertainty. These issues challenge the view that genomic research on human beings can (or should) be fully segregated from clinical genomics, either conceptually or practically. Here we argue that the historical sharp distinction between clinical care and research is especially problematic in the context of large-scale genomic sequencing of people with suspected genetic conditions. Core goals of both enterprises (e.g., understanding genotype-phenotype relationships; generating an evidence base for genomic medicine) are more likely to be realized at a population scale if both those ordering and those undergoing sequencing for clinical reasons are routinely and longitudinally studied. Rather than relying on expensive and lengthy randomized clinical trials and meta-analyses, we propose leveraging nascent clinical-research hybrid frameworks into a broader, more permanent instantiation of exploratory medical sequencing. Such an investment could enlighten stakeholders about the real-life challenges posed by whole-genome sequencing, e.g., establishing the clinical actionability of genetic variants, returning “off-target” results to families, developing effective service delivery models and monitoring long-term outcomes. PMID:25045831

  9. Genome Sequence of Gordonia Bacteriophage Lucky10

    PubMed Central

    Brown, Aleks K.; Fisher, Daniel J.; Okwiya, Nicholas H.; Savage, Kaitlyn A.; German, Brian A.; McDonnell, Jill E.; Schafer, Claire E.; Yu, Victor J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Lucky10 is a newly isolated phage of Gordonia terrae 3612 that was recovered from a soil sample in Pittsburgh, PA. Lucky10 has siphoviral morphology and a double-stranded DNA (dsDNA) genome of 42,979 bp, with 70 predicted protein-coding genes. Lucky10 shows little similarity to previously reported Gordonia phages. PMID:27365346

  10. Draft genome sequences of two virulent serotypes of avian Pasteurella multocida

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we report the draft genome sequences of two virulent avian strains of Pasteurella multocida. Comparative analyses of these genomes were done with the published genome sequence of avirulent Pasteurella multocida strain Pm70....

  11. Pervasive sequence patents cover the entire human genome.

    PubMed

    Rosenfeld, Jeffrey A; Mason, Christopher E

    2013-01-01

    The scope and eligibility of patents for genetic sequences have been debated for decades, but a critical case regarding gene patents (Association of Molecular Pathologists v. Myriad Genetics) is now reaching the US Supreme Court. Recent court rulings have supported the assertion that such patents can provide intellectual property rights on sequences as small as 15 nucleotides (15mers), but an analysis of all current US patent claims and the human genome presented here shows that 15mer sequences from all human genes match at least one other gene. The average gene matches 364 other genes as 15mers; the breast-cancer-associated gene BRCA1 has 15mers matching at least 689 other genes. Longer sequences (1,000 bp) still showed extensive cross-gene matches. Furthermore, 15mer-length claims from bovine and other animal patents could also claim as much as 84% of the genes in the human genome. In addition, when we expanded our analysis to full-length patent claims on DNA from all US patents to date, we found that 41% of the genes in the human genome have been claimed. Thus, current patents for both short and long nucleotide sequences are extraordinarily non-specific and create an uncertain, problematic liability for genomic medicine, especially in regard to targeted re-sequencing and other sequence diagnostic assays. PMID:23522065

  12. Systematic genome sequence differences among leaf cells within individual trees

    PubMed Central

    2014-01-01

    Background Even in the age of next-generation sequencing (NGS), it has been unclear whether or not cells within a single organism have systematically distinctive genomes. Resolving this question, one of the most basic biological problems associated with DNA mutation rates, can assist efforts to elucidate essential mechanisms of cancer. Results Using genome profiling (GP), we detected considerable systematic variation in genome sequences among cells in individual woody plants. The degree of genome sequence difference (genomic distance) varied systematically from the bottom to the top of the plant, such that the greatest divergence was observed between leaf genomes from uppermost branches and the remainder of the tree. This systematic variation was observed within both Yoshino cherry and Japanese beech trees. Conclusions As measured by GP, the genomic distance between two cells within an individual organism was non-negligible, and was correlated with physical distance (i.e., branch-to-branch distance). This phenomenon was assumed to be the result of accumulation of mutations from each cell division, implying that the degree of divergence is proportional to the number of generations separating the two cells. PMID:24548431

  13. Adaptive seeds tame genomic sequence comparison.

    PubMed

    Kiełbasa, Szymon M; Wan, Raymond; Sato, Kengo; Horton, Paul; Frith, Martin C

    2011-03-01

    The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. PMID:21209072

  14. Evolution Analysis of Simple Sequence Repeats in Plant Genome

    PubMed Central

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution. PMID:26630570

  15. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

    PubMed Central

    2010-01-01

    Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems. PMID:20186266

  16. Genomic Sequence or Signature Tags (GSTs) from the Genome Group at Brookhaven National Laboratory (BNL)

    DOE Data Explorer

    Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; Van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K.

    Genomic Signature Tags (GSTs) are the products of a method we have developed for identifying and quantitatively analyzing genomic DNAs. The DNA is initially fragmented with a type II restriction enzyme. An oligonucleotide adaptor containing a recognition site for MmeI, a type IIS restriction enzyme, is then used to release 21-bp tags from fixed positions in the DNA relative to the sites recognized by the fragmenting enzyme. These tags are PCR-amplified, purified, concatenated and then cloned and sequenced. The tag sequences and abundances are used to create a high resolution GST sequence profile of the genomic DNA. [Quoted from Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA, Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; Van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K., Revised 9/13/2002

  17. Whole-genome haplotyping by dilution, amplification, and sequencing

    PubMed Central

    Kaper, Fiona; Swamy, Sajani; Klotzle, Brandy; Munchel, Sarah; Cottrell, Joseph; Bibikova, Marina; Chuang, Han-Yu; Kruglyak, Semyon; Ronaghi, Mostafa; Eberle, Michael A.; Fan, Jian-Bing

    2013-01-01

    Standard whole-genome genotyping technologies are unable to determine haplotypes. Here we describe a method for rapid and cost-effective long-range haplotyping. Genomic DNA is diluted and distributed into multiple aliquots such that each aliquot receives a fraction of a haploid copy. The DNA template in each aliquot is amplified by multiple displacement amplification, converted into barcoded sequencing libraries using Nextera technology, and sequenced in multiplexed pools. To assess the performance of our method, we combined two male genomic DNA samples at equal ratios, resulting in a sample with diploid X chromosomes with known haplotypes. Pools of the multiplexed sequencing libraries were subjected to targeted pull-down of a 1-Mb contiguous region of the X-chromosome Duchenne muscular dystrophy gene. We were able to phase the Duchenne muscular dystrophy region into two contiguous haplotype blocks with a mean length of 494 kb. The haplotypes showed 99% agreement with the consensus base calls made by sequencing the individual DNAs. We subsequently used the strategy to haplotype two human genomes. Standard genomic sequencing to identify all heterozygous SNPs in the sample was combined with dilution-amplification–based sequencing data to resolve the phase of identified heterozygous SNPs. Using this procedure, we were able to phase >95% of the heterozygous SNPs from the diploid sequence data. The N50 for a Yoruba male DNA was 702 kb whereas the N50 for a European female DNA was 358 kb. Therefore, the strategy described here is suitable for haplotyping of a set of targeted regions as well as of the entire genome. PMID:23509297

  18. Whole-genome haplotyping by dilution, amplification, and sequencing.

    PubMed

    Kaper, Fiona; Swamy, Sajani; Klotzle, Brandy; Munchel, Sarah; Cottrell, Joseph; Bibikova, Marina; Chuang, Han-Yu; Kruglyak, Semyon; Ronaghi, Mostafa; Eberle, Michael A; Fan, Jian-Bing

    2013-04-01

    Standard whole-genome genotyping technologies are unable to determine haplotypes. Here we describe a method for rapid and cost-effective long-range haplotyping. Genomic DNA is diluted and distributed into multiple aliquots such that each aliquot receives a fraction of a haploid copy. The DNA template in each aliquot is amplified by multiple displacement amplification, converted into barcoded sequencing libraries using Nextera technology, and sequenced in multiplexed pools. To assess the performance of our method, we combined two male genomic DNA samples at equal ratios, resulting in a sample with diploid X chromosomes with known haplotypes. Pools of the multiplexed sequencing libraries were subjected to targeted pull-down of a 1-Mb contiguous region of the X-chromosome Duchenne muscular dystrophy gene. We were able to phase the Duchenne muscular dystrophy region into two contiguous haplotype blocks with a mean length of 494 kb. The haplotypes showed 99% agreement with the consensus base calls made by sequencing the individual DNAs. We subsequently used the strategy to haplotype two human genomes. Standard genomic sequencing to identify all heterozygous SNPs in the sample was combined with dilution-amplification-based sequencing data to resolve the phase of identified heterozygous SNPs. Using this procedure, we were able to phase >95% of the heterozygous SNPs from the diploid sequence data. The N50 for a Yoruba male DNA was 702 kb whereas the N50 for a European female DNA was 358 kb. Therefore, the strategy described here is suitable for haplotyping of a set of targeted regions as well as of the entire genome. PMID:23509297

  19. Toward Complete Bacterial Genome Sequencing Through the Combined Use of Multiple Next-Generation Sequencing Platforms.

    PubMed

    Jeong, Haeyoung; Lee, Dae-Hee; Ryu, Choong-Min; Park, Seung-Hwan

    2016-01-01

    PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of secondgeneration, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction. PMID:26464377

  20. Sequencing the yeast genome: the European effort.

    PubMed

    Vassarotti, A; Goffeau, A

    1992-01-01

    For ethical, practical and economic reasons, scientists have traditionally relied on model organisms for biological research. Although model organisms do not always quite constitute the 'real thing', the significant advantages of their use contribute to making their study a viable alternative. The decision to use a specific model, particularly in large-scale studies such as genome projects, will be governed not only by biological consideration, but also by the prevailing financial and organizational infrastructure and expertise of the research community. PMID:1367925

  1. Genome Sequencing Fishes out Longevity Genes.

    PubMed

    Lakhina, Vanisha; Murphy, Coleen T

    2015-12-01

    Understanding the molecular basis underlying aging is critical if we are to fully understand how and why we age-and possibly how to delay the aging process. Up until now, most longevity pathways were discovered in invertebrates because of their short lifespans and availability of genetic tools. Now, Reichwald et al. and Valenzano et al. independently provide a reference genome for the short-lived African turquoise killifish, establishing its role as a vertebrate system for aging research. PMID:26638067

  2. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    FitzGerald, Michael [Broad Institute

    2013-02-12

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  3. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    SciTech Connect

    FitzGerald, Michael

    2012-06-01

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  4. Strong nucleosomes of mouse genome including recovered centromeric sequences.

    PubMed

    Salih, Bilal F; Teif, Vladimir B; Tripathi, Vijay; Trifonov, Edward N

    2015-01-01

    Recently discovered strong nucleosomes (SNs) characterized by visibly periodical DNA sequences have been found to concentrate in centromeres of Arabidopsis thaliana and in transient meiotic centromeres of Caenorhabditis elegans. To find out whether such affiliation of SNs to centromeres is a more general phenomenon, we studied SNs of the Mus musculus. The publicly available genome sequences of mouse, as well as of practically all other eukaryotes do not include the centromere regions which are difficult to assemble because of a large amount of repeat sequences in the centromeres and pericentromeric regions. We recovered those missing sequences using the data from MNase-seq experiments in mouse embryonic stem cells, where the sequence of DNA inside nucleosomes, including missing regions, was determined by 100-bp paired-end sequencing. Those nucleosome sequences, which are not matching to the published genome sequence, would largely belong to the centromeres. By evaluating SN densities in centromeres and in non-centromeric regions, we conclude that mouse SNs concentrate in the centromeres of telocentric mouse chromosomes, with ~3.9 times excess compared to their density in the rest of the genome. The remaining non-centromeric SNs are harbored mainly by introns and intergenic regions, by retro-transposons, in particular. The centromeric involvement of the SNs opens new horizons for the chromosome and centromere structure studies. PMID:24998943

  5. Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism

    PubMed Central

    Millar, Scott B.; Sanderson, Theo; Otto, Thomas D.; Lu, Woon Chan; Krishna, Sanjeev; Rayner, Julian C.; Cox-Singh, Janet

    2015-01-01

    Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology. PMID:25830531

  6. The International Pea Genome Sequencing Project: Sequencing and Assembly Progresses Updates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The International Consortium for the Pea Genome Sequencing (ICPG) includes scientists from six countries around the world. Its aim is to provide a high quality reference of the pea genome to the scientific community as well as to the pea breeder community. The consortium proposed a strategy that int...

  7. Whole genome sequencing in clinical and public health microbiology

    PubMed Central

    Kwong, J. C.; McCallum, N.; Sintchenko, V.; Howden, B. P.

    2015-01-01

    SummaryGenomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology. The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology. Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories. As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future. Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure. PMID:25730631

  8. Complete genome sequence of Meiothermus ruber type strain (21T)

    SciTech Connect

    Tindall, Brian; Sikorski, Johannes; Lucas, Susan; Goltsman, Eugene; Copeland, A; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Fahnrich, Regine; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2010-01-01

    Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members can be affiliated to either low-temperature or high-temperature groups. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. The complete plastid genome sequence of Bomarea edulis (Alstroemeriaceae: Liliales).

    PubMed

    Kim, Jung Sung; Kim, Hyoung Tae; Yoon, Chang Young; Kim, Joo-Hwan

    2016-05-01

    Bomarea, a member of the family Alstroemeriaceae, is distributed from Chile to Mexico and includes approximately 120 species. Recent molecular phylogenetic studies have clarified the monophyly of the family within the order Liliales and the sister relationship with the family Colchicaceae. At this time, five plastid genomes of Liliales have been analyzed at the familial level. To examine plastid genome variation at the generic level, we sequenced the plastid genome of Bomarea edulis, which is the most widely distributed species in the genus, and compared it with Alstroemeria aurea. The plastid genome sequence of B. edulis was 154,925 bp in length with a similar structure as A. aurea, excluding the IR-LSC junction. Ycf68 and infA were pseudogenes caused by frameshift mutations, and the ycf15 gene was deleted, similar to A. aurea. PMID:25319309

  10. Complete genome sequence of Arthrobacter sp. strain FB24

    SciTech Connect

    Nakatsu, C. H.; Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, T.; Han, Cliff F.; Beasley, Federico; Chen, Weimin; Konopka, Allan; Xie, Gary

    2013-09-30

    Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

  11. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575).

    PubMed

    Spring, Stefan; Lapidus, Alla; Schröder, Maren; Gleim, Dorothea; Sims, David; Meincke, Linda; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Saunders, Elizabeth; Brettin, Thomas; Detter, John C; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-01-01

    Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575(T), isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304664

  12. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)

    PubMed Central

    Spring, Stefan; Lapidus, Alla; Schröder, Maren; Gleim, Dorothea; Sims, David; Meincke, Linda; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Saunders, Elizabeth; Brettin, Thomas; Detter, John C.; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-01-01

    Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575T, isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304664

  13. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)

    SciTech Connect

    Spring, Stefan; Lapidus, Alla L.; Schroder, Maren; Gleim, Dorothea; Sims, David; Meincke, Linda; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Lucas, Susan; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Brettin, Tom; Detter, J. Chris; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-01-01

    Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575T, isolated from piggery waste in Germany. Here we describe the features of this organ-ism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis.

    PubMed

    Duan, Naibin; Sun, Honghe; Wang, Nan; Fei, Zhangjun; Chen, Xuesen

    2016-07-01

    The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis, a widely used apple rootstock, was determined using the Illumina high-throughput sequencing approach. The genome is 422,555 bp in length and has a GC content of 45.21%. It is separated by a pair of inverted repeats of 32,504 bp, to form a large single copy region of 213,055 bp and a small single copy region of 144,492 bp. The genome contains 38 protein-coding genes, four pseudogenes, 25 tRNA genes, and three rRNA genes. The genome is 25,608 bp longer than that of M. domestica, and several structural variations between these two mitogenomes were detected. PMID:26539696

  15. Genome rearrangements caused by interstitial telomeric sequences in yeast

    PubMed Central

    Aksenova, Anna Y.; Greenwell, Patricia W.; Dominska, Margaret; Shishkin, Alexander A.; Kim, Jane C.; Petes, Thomas D.; Mirkin, Sergei M.

    2013-01-01

    Interstitial telomeric sequences (ITSs) are present in many eukaryotic genomes and are linked to genome instabilities and disease in humans. The mechanisms responsible for ITS-mediated genome instability are not understood in molecular detail. Here, we use a model Saccharomyces cerevisiae system to characterize genome instability mediated by yeast telomeric (Ytel) repeats embedded within an intron of a reporter gene inside a yeast chromosome. We observed a very high rate of small insertions and deletions within the repeats. We also found frequent gross chromosome rearrangements, including deletions, duplications, inversions, translocations, and formation of acentric minichromosomes. The inversions are a unique class of chromosome rearrangement involving an interaction between the ITS and the true telomere of the chromosome. Because we previously found that Ytel repeats cause strong replication fork stalling, we suggest that formation of double-stranded DNA breaks within the Ytel sequences might be responsible for these gross chromosome rearrangements. PMID:24191060

  16. Complete genome sequence of Arthrobacter sp. strain FB24

    PubMed Central

    Nakatsu, Cindy H.; Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, Thomas; Han, Cliff; Beasley, Federico; Chen, Weimin; Konopka, Allan; Xie, Gary

    2013-01-01

    Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program. PMID:24501649

  17. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)

    SciTech Connect

    Mavromatis, K; Sikorski, Johannes; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Meincke, Linda; Sims, David; Chertkov, Olga; Han, Cliff; Brettin, Tom; Detter, J C; Wahrenburg, Claudia; Rohde, Manfred; Pukall, Rudiger; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family Alicyclobacillaceae . A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Alicyclobacillaceae . The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.

    PubMed

    Ockendon, Nina F; O'Connell, Lauren A; Bush, Stephen J; Monzón-Sandoval, Jimena; Barnes, Holly; Székely, Tamás; Hofmann, Hans A; Dorus, Steve; Urrutia, Araxi O

    2016-03-01

    Next-generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly-based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that DGM recovers a more representative profile of Gene Ontology functional categories, which are often used to interpret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA-seq data demonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy and reduced gene detection associated with sequence divergence thus provides empirically derived guidelines for the design of future gene expression studies in species without sequenced genomes. PMID:26358618

  19. Accuracy of genomic prediction using imputed whole-genome sequence data in white layers.

    PubMed

    Heidaritabar, M; Calus, M P L; Megens, H-J; Vereijken, A; Groenen, M A M; Bastiaansen, J W M

    2016-06-01

    There is an increasing interest in using whole-genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole-genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole-genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non-synonymous and non-coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non-synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data. PMID:26776363

  20. Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies

    PubMed Central

    Thibessard, Annabelle

    2016-01-01

    The sequence of Streptomyces ambofaciens DSM 40697 was completely determined. The genome consists of an 8.1-Mbp linear chromosome with terminal inverted repeats of 210 kb. Genomic islands were identified, one of which corresponds to a new putative integrative and conjugative element (ICE) called pSAM3. PMID:27257195

  1. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

    PubMed Central

    Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark; Gailing, Oliver; Liang, Haiying; Romero-Severson, Jeanne; Schlarbaum, Scott; Carlson, John E.

    2015-01-01

    Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence. PMID:26698853

  2. Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies.

    PubMed

    Thibessard, Annabelle; Leblond, Pierre

    2016-01-01

    The sequence of Streptomyces ambofaciens DSM 40697 was completely determined. The genome consists of an 8.1-Mbp linear chromosome with terminal inverted repeats of 210 kb. Genomic islands were identified, one of which corresponds to a new putative integrative and conjugative element (ICE) called pSAM3. PMID:27257195

  3. The power of EST sequence data: Relation to Acyrthosiphon pisum genome annotation and functional genomics initiatives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genes important to aphid biology, survival and reproduction were successfully identified by use of a genomics approach. We created and described the Sequencing, compilation, and annotation of the approxiamtely 525Mb nuclear genome of the pea aphid, Acyrthosiphon pisum, which represents an important ...

  4. Complete Genome Sequence of Pediococcus pentosaceus Strain SL4

    PubMed Central

    Dantoft, Shruti Harnal; Bielak, Eliza Maria; Seo, Jae-Gu; Chung, Myung-Jun

    2013-01-01

    Pediococcus pentosaceus SL4 was isolated from a Korean fermented vegetable product, kimchi. We report here the whole-genome sequence (WGS) of P. pentosaceus SL4. The genome consists of a 1.79-Mb circular chromosome (G+C content of 37.3%) and seven distinct plasmids ranging in size from 4 kb to 50 kb. PMID:24371205

  5. Complete Genome Sequence of the Endophytic Fungus Diaporthe (Phomopsis) ampelina

    PubMed Central

    Bhargavi, S. D.; Praveen, V. K.

    2016-01-01

    Diaporthe ampelina was isolated as an endophytic fungus from the root of Commiphora wightii, a medicinal plant collected from Dhanvantri Vana, Bangalore University, Bangalore, India. The whole genome is 59 Mb, contains a total of 905 scaffolds, and has a G+C content of 51.74%. The genome sequence of D. ampelina shows a complete absence of lovastatin (an anticholesterol drug) gene cluster. PMID:27257198

  6. Complete genome sequence of Croceibacter atlanticus HTCC2559T.

    PubMed

    Oh, Hyun-Myung; Kang, Ilnam; Ferriera, Steve; Giovannoni, Stephen J; Cho, Jang-Cheon

    2010-09-01

    Here we announce the complete genome sequence of Croceibacter atlanticus HTCC2559(T), which was isolated by high-throughput dilution-to-extinction culturing from the Bermuda Atlantic Time Series station in the Western Sargasso Sea. Strain HTCC2559(T) contained genes for carotenoid biosynthesis, flavonoid biosynthesis, and several macromolecule-degrading enzymes. The genome confirmed physiological observations of cultivated Croceibacter atlanticus strain HTCC2559(T), which identified it as an obligate chemoheterotroph. PMID:20639333

  7. Genome Sequence of Corynebacterium ulcerans Strain FRC11

    PubMed Central

    Benevides, Leandro de Jesus; Viana, Marcus Vinicius Canário; Mariano, Diego César Batista; Rocha, Flávia de Souza; Bagano, Priscilla Carolinne; Folador, Edson Luiz; Pereira, Felipe Luiz; Dorella, Fernanda Alves; Leal, Carlos Augusto Gomes; Carvalho, Alex Fiorini; Soares, Siomar de Castro; Carneiro, Adriana; Ramos, Rommel; Badell-Ocando, Edgar; Guiso, Nicole; Silva, Artur; Figueiredo, Henrique; Guimarães, Luis Carlos

    2015-01-01

    Here, we present the genome sequence of Corynebacterium ulcerans strain FRC11. The genome includes one circular chromosome of 2,442,826 bp (53.35% G+C content), and 2,210 genes were predicted, 2,146 of which are putative protein-coding genes, with 12 rRNAs and 51 tRNAs; 1 pseudogene was also identified. PMID:25767241

  8. Complete Genome Sequence of the Endophytic Fungus Diaporthe (Phomopsis) ampelina.

    PubMed

    Savitha, J; Bhargavi, S D; Praveen, V K

    2016-01-01

    Diaporthe ampelina was isolated as an endophytic fungus from the root of Commiphora wightii, a medicinal plant collected from Dhanvantri Vana, Bangalore University, Bangalore, India. The whole genome is 59 Mb, contains a total of 905 scaffolds, and has a G+C content of 51.74%. The genome sequence of D. ampelina shows a complete absence of lovastatin (an anticholesterol drug) gene cluster. PMID:27257198

  9. Complete Genome Sequence of Klebsiella pneumoniae YH43

    PubMed Central

    Ogura, Yoshitoshi; Hayashi, Tetsuya; Mizunoe, Yoshimitsu

    2016-01-01

    We report here the complete genome sequence of Klebsiella pneumoniae strain YH43, isolated from sweet potato. The genome consists of a single circular chromosome of 5,520,319 bp in length. It carries 8 copies of rRNA operons, 86 tRNA genes, 5,154 protein-coding genes, and the nif gene cluster for nitrogen fixation. PMID:27081127

  10. Contribution to Sequencing of the Deinococcus radiodurans Genome

    SciTech Connect

    Minton, K.W.

    1999-03-11

    The stated goal of this project was to supply The Institute for Genomic Research (TIGR) with pure DNA from the bacterium Deinocmus radiodurans RI for purposes of complete genomic sequencing by TIGR. We subsequently decided to expand this project to include a second goal; this second goal was the development of a NotI chromosomal map of D. radiodurans R1 using Pulsed Field Gel Electrophoresis (PFGE).

  11. The complete genome sequence of Escherichia coli K-12.

    PubMed

    Blattner, F R; Plunkett, G; Bloch, C A; Perna, N T; Burland, V; Riley, M; Collado-Vides, J; Glasner, J D; Rode, C K; Mayhew, G F; Gregor, J; Davis, N W; Kirkpatrick, H A; Goeden, M A; Rose, D J; Mau, B; Shao, Y

    1997-09-01

    The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer. PMID:9278503

  12. Draft genome sequence of Fusicladium effusum, cause of pecan scab.

    PubMed

    Bock, Clive H; Chen, Chunxian; Yu, Fahong; Stevenson, Katherine L; Wood, Bruce W

    2016-01-01

    Pecan scab, caused by the plant pathogenic fungus Fusicladium effusum, is the most destructive disease of pecan, an important specialty crop cultivated in several regions of the world. Only a few members of the family Venturiaceae (in which the pathogen resides) have been reported sequenced. We report the first draft genome sequence (40.6 Mb) of an isolate F. effusum collected from a pecan tree (cv. Desirable) in central Georgia, in the US. The genome sequence described will be a useful resource for research of the biology and ecology of the pathogen, coevolution with the pecan host, characterization of genes of interest, and development of markers for studies of genetic diversity, genotyping and phylogenetic analysis. The annotation of the genome is described and a phylogenetic analysis is presented. PMID:27274782

  13. Exploring genome characteristics and sequence quality without a reference

    PubMed Central

    2014-01-01

    Motivation: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly. Results: This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty. Availability: The software described is freely available online (https://github.com/jts/sga) and open source under the GNU Public License. Contact: jared.simpson@oicr.on.ca Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24443382

  14. A Complete Sequence of the T. tengcongensis Genome

    PubMed Central

    Bao, Qiyu; Tian, Yuqing; Li, Wei; Xu, Zuyuan; Xuan, Zhenyu; Hu, Songnian; Dong, Wei; Yang, Jian; Chen, Yanjiong; Xue, Yanfen; Xu, Yi; Lai, Xiaoqin; Huang, Li; Dong, Xiuzhu; Ma, Yanhe; Ling, Lunjiang; Tan, Huarong; Chen, Runsheng; Wang, Jian; Yu, Jun; Yang, Huanming

    2002-01-01

    Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we sequenced its 2,689,445-bp genome from an isolate, MB4T (Genbank accession no. AE008691). The genome encodes 2588 predicted coding sequences (CDS). Among them, 1764 (68.2%) are classified according to homology to other documented proteins, and the rest, 824 CDS (31.8%), are functionally unknown. One of the interesting features of the T. tengcongensis genome is that 86.7% of its genes are encoded on the leading strand of DNA replication. Based on protein sequence similarity, the T. tengcongensis genome is most similar to that of Bacillus halodurans, a mesophilic eubacterium, among all fully sequenced prokaryotic genomes up to date. Computational analysis on genes involved in basic metabolic pathways supports the experimental discovery that T. tengcongensis metabolizes sugars as principal energy and carbon source and utilizes thiosulfate and element sulfur, but not sulfate, as electron acceptors. T. tengcongensis, as a gram-negative rod by empirical definitions (such as staining), shares many genes that are characteristics of gram-positive bacteria whereas it is missing molecular components unique to gram-negative bacteria. A strong correlation between the G + C content of tDNA and rDNA genes and the optimal growth temperature is found among the sequenced thermophiles. It is concluded that thermophiles are a biologically and phylogenetically divergent group of prokaryotes that have converged to sustain extreme environmental conditions over evolutionary timescale. [Supplemental material is available online at http://www.genome.org.] PMID:11997336

  15. Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

    PubMed Central

    Staats, Martijn; Erkens, Roy H. J.; van de Vossenberg, Bart; Wieringa, Jan J.; Kraaijeveld, Ken; Stielow, Benjamin; Geml, József; Richardson, James E.; Bakker, Freek T.

    2013-01-01

    Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more

  16. Standardized metadata for human pathogen/vector genomic sequences.

    PubMed

    Dugan, Vivien G; Emrich, Scott J; Giraldo-Calderón, Gloria I; Harb, Omar S; Newman, Ruchi M; Pickett, Brett E; Schriml, Lynn M; Stockwell, Timothy B; Stoeckert, Christian J; Sullivan, Dan E; Singh, Indresh; Ward, Doyle V; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H; Cuomo, Christina A; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W Florian; Giovanni, Maria; Henn, Matthew R; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F; Murphy, Cheryl I; Myers, Garry; Neafsey, Daniel E; Nelson, Karen E; Nierman, William C; Puzak, Julia; Rasko, David; Roos, David S; Sadzewicz, Lisa; Silva, Joana C; Sobral, Bruno; Squires, R Burke; Stevens, Rick L; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H

    2014-01-01

    High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a

  17. Standardized Metadata for Human Pathogen/Vector Genomic Sequences

    PubMed Central

    Dugan, Vivien G.; Emrich, Scott J.; Giraldo-Calderón, Gloria I.; Harb, Omar S.; Newman, Ruchi M.; Pickett, Brett E.; Schriml, Lynn M.; Stockwell, Timothy B.; Stoeckert, Christian J.; Sullivan, Dan E.; Singh, Indresh; Ward, Doyle V.; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M.; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H.; Cuomo, Christina A.; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W. Florian; Giovanni, Maria; Henn, Matthew R.; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C.; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F.; Murphy, Cheryl I.; Myers, Garry; Neafsey, Daniel E.; Nelson, Karen E.; Nierman, William C.; Puzak, Julia; Rasko, David; Roos, David S.; Sadzewicz, Lisa; Silva, Joana C.; Sobral, Bruno; Squires, R. Burke; Stevens, Rick L.; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H.

    2014-01-01

    High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a

  18. Transcription of densovirus endogenous sequences in the Myzus persicae genome.

    PubMed

    Clavijo, Gabriel; van Munster, Manuella; Monsion, Baptiste; Bochet, Nicole; Brault, Véronique

    2016-04-01

    Integration of non-retroviral sequences in the genome of different organisms has been observed and, in some cases, a relationship of these integrations with immunity has been established. The genome of the green peach aphid, Myzus persicae (clone G006), was screened for densovirus-like sequence (DLS) integrations. A total of 21 DLSs localized on 10 scaffolds were retrieved that mostly shared sequence identity with two aphid-infecting viruses, Myzus persicae densovirus (MpDNV) and Dysaphis plantaginea densovirus (DplDNV). In some cases, uninterrupted potential ORFs corresponding to non-structural viral proteins or capsid proteins were found within DLSs identified in the aphid genome. In particular, one scaffold harboured a complete virus-like genome, while another scaffold contained two virus-like genomes in reverse orientation. Remarkably, transcription of some of these ORFs was observed in M. persicae, suggesting a biological effect of these viral integrations. In contrast to most of the other densoviruses identified so far that induce acute host infection, it has been reported previously that MpDNV has only a minor effect on M. persicae fitness, while DplDNV can even have a beneficial effect on its aphid host. This suggests that DLS integration in the M. persicae genome may be responsible for the latency of MpDNV infection in the aphid host. PMID:26758080

  19. The genome sequence of the colonial chordate, Botryllus schlosseri

    PubMed Central

    Voskoboynik, Ayelet; Neff, Norma F; Sahoo, Debashis; Newman, Aaron M; Pushkarev, Dmitry; Koh, Winston; Passarelli, Benedetto; Fan, H Christina; Mantalas, Gary L; Palmeri, Karla J; Ishizuka, Katherine J; Gissi, Carmela; Griggio, Francesca; Ben-Shlomo, Rachel; Corey, Daniel M; Penland, Lolita; White, Richard A; Weissman, Irving L; Quake, Stephen R

    2013-01-01

    Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration. DOI: http://dx.doi.org/10.7554/eLife.00569.001 PMID:23840927

  20. Genome sequence of the human malaria parasite Plasmodium falciparum

    PubMed Central

    Gardner, Malcolm J.; Hall, Neil; Fung, Eula; White, Owen; Berriman, Matthew; Hyman, Richard W.; Carlton, Jane M.; Pain, Arnab; Nelson, Karen E.; Bowman, Sharen; Paulsen, Ian T.; James, Keith; Eisen, Jonathan A.; Rutherford, Kim; Salzberg, Steven L.; Craig, Alister; Kyes, Sue; Chan, Man-Suen; Nene, Vishvanath; Shallom, Shamira J.; Suh, Bernard; Peterson, Jeremy; Angiuoli, Sam; Pertea, Mihaela; Allen, Jonathan; Selengut, Jeremy; Haft, Daniel; Mather, Michael W.; Vaidya, Akhil B.; Martin, David M. A.; Fairlamb, Alan H.; Fraunholz, Martin J.; Roos, David S.; Ralph, Stuart A.; McFadden, Geoffrey I.; Cummings, Leda M.; Subramanian, G. Mani; Mungall, Chris; Venter, J. Craig; Carucci, Daniel J.; Hoffman, Stephen L.; Newbold, Chris; Davis, Ronald W.; Fraser, Claire M.; Barrell, Bart

    2013-01-01

    The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host–parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria. PMID:12368864

  1. The complete mitochondrial genome sequence of the budgerigar, Melopsittacus undulatus.

    PubMed

    Guan, Xiaojing; Xu, Jun; Smith, Edward J

    2016-01-01

    Here, we describe the budgie's mitochondrial genome sequence, a resource that can facilitate this parrot's use as a model organism as well as for determining its phylogenetic relatedness to other parrots/Psittaciformes. The estimated total length of the sequence was 18,193 bp. In addition to the to the 13 protein and tRNA and rRNA coding regions, the sequence also includes a duplicated hypervariable region, a feature unique to only a few birds. The two hypervariable regions shared a sequence identity of about 86%. PMID:24660934

  2. Pittosporum cryptic virus 1: genome sequence completion using next-generation sequencing.

    PubMed

    Elbeaino, Toufic; Kubaa, Raied Abou; Tuzlali, Hasan Tuna; Digiaro, Michele

    2016-07-01

    Next-generation sequencing (NGS) was applied to dsRNAs extracted from an Italian pittosporum plant infected with pittosporum cryptic virus 1 (PiCV1). NGS allowed assembly of the full genome sequence of PiCV1, comprising dsRNA1 (1.9 kbp) and dsRNA2 (1.5 kbp), which encode the RNA-dependent RNA polymerase and capsid protein genes, respectively. Phylogenetic and sequence analyses confirmed that PiCV1 is a new member of the genus Deltapartitivirus, family Partiviridae. From the same plant, NSG also permitted assembly of the complete genome sequence of eggplant mottled dwarf virus (EMDV), which shared 86 % to 98 % nucleotide sequence identity with complete and partial sequences (ca 6750 nt) of other known EMDV isolates with sequences available in the GenBank database. PMID:27087112

  3. Genome Sequence of Propionibacterium acidipropionici ATCC 55737.

    PubMed

    Luna-Flores, Carlos H; Nielsen, Lars K; Marcellin, Esteban

    2016-01-01

    Propionibacterium acidipropionici produces propionic acid as its main fermentation product. Traditionally derived from fossil fuels, environmental and sustainable issues have revived the interest in producing propionic acid using biological resources. Here, we present the closed sequence of Propionibacterium acidipropionici ATCC 55737, an efficient propionic acid producer. PMID:27198010

  4. The complete chloroplast genome sequence of Amentotaxus argotaenia (Taxaceae).

    PubMed

    Li, Jia; Gao, Lei; Tao, Ke; Su, Yingjuan; Wang, Ting

    2016-07-01

    The complete chloroplast genome sequence of Amentotaxus argotaenia was determined in this study. The genome is 136 657 bp in length and lacks one inverted repeat region. The overall GC content of the genome is 35.85% (protein-coding genes, 36.90%; tRNA genes, 53.31%; rRNA genes, 52.99%; introns, 36.10%; intergenic spacers, 31.03%). The A. argotaenia chloroplast genome contains 118 unique genes, including 83 protein-coding genes, 31 tRNA genes, and four rRNA genes. Ten protein-coding genes and six tRNA genes have one intron, while ycf3 contains two. The coding regions occupy 60.27% of the genome length and the gene density is estimated to be 0.88 genes/kb. A maximum likelihood phylogenetic analysis suggested that Amentotaxus is sister to Taxus within the Taxaceae family. PMID:26119122

  5. Complete genome sequence of Haliscomenobacter hydrossis type strain (OT)

    SciTech Connect

    Daligault, Hajnalka E.; Lapidus, Alla L.; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Huntemann, Marcel; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Verbarg, Susanne; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2011-01-01

    Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Halisco- menobacter, which belongs to order 'Sphingobacteriales'. The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically un- charted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family 'Saprospiraceae'. The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Genome Sequencing and Annotation of Mycobacterium tuberculosis PR08 strain.

    PubMed

    Jaafar, Mohammad Maaruf; Halim, Mohd Zakihalani A; Ismail, Mohamad Izwan; Shien, Lee Lian; Kek, Teh Lay; Fong, Ngeow Yun; Nor, Norazmi Mohd; Zainuddin, Zainul Fadziruddin; Hock, Tang Thean; Najimudin, Mohd Nazalan Mohd; Salleh, Mohd Zaki

    2016-03-01

    Mycobacterium tuberculosis is an acid fast bacterial species in the family Mycobacteriaceae and is the causative agent of most cases of tuberculosis. Here, we report the genomic features of Mycobacterium tuberculosis isolated from the cerebrospinal fluid (CSF) of a patient diagnosed with both pulmonary and extrapulmonary tuberculosis (TB). The isolated strain was identified as Mycobacterium tuberculosis PR08 (MTB PR08). Genomic DNA of the MTB PR08 strain was extracted and subjected to whole genome sequencing using MiSeq (Illumina, CA,USA). The draft genome size of MTB PR08 strain is 4,292,364 bp with a G + C content of 65.2%. This strain was annotated to have 4723 genes and 48 RNAs. This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010895. PMID:26981383

  7. A cryptographic approach to securely share and query genomic sequences.

    PubMed

    Kantarcioglu, Murat; Jiang, Wei; Liu, Ying; Malin, Bradley

    2008-09-01

    To support large-scale biomedical research projects, organizations need to share person-specific genomic sequences without violating the privacy of their data subjects. In the past, organizations protected subjects' identities by removing identifiers, such as name and social security number; however, recent investigations illustrate that deidentified genomic data can be "reidentified" to named individuals using simple automated methods. In this paper, we present a novel cryptographic framework that enables organizations to support genomic data mining without disclosing the raw genomic sequences. Organizations contribute encrypted genomic sequence records into a centralized repository, where the administrator can perform queries, such as frequency counts, without decrypting the data. We evaluate the efficiency of our framework with existing databases of single nucleotide polymorphism (SNP) sequences and demonstrate that the time needed to complete count queries is feasible for real world applications. For example, our experiments indicate that a count query over 40 SNPs in a database of 5000 records can be completed in approximately 30 min with off-the-shelf technology. We further show that approximation strategies can be applied to significantly speed up query execution times with minimal loss in accuracy. The framework can be implemented on top of existing information and network technologies in biomedical environments. PMID:18779075

  8. Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis

    PubMed Central

    Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; Liu, Xinyue; Melake-Berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom-Sternberg, Stephen M.; Allan, Gerard J.; Keim, Paul; Ravel, Jacques; Rabinowicz, Pablo D.

    2011-01-01

    Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade. PMID:21750729

  9. Genome sequence and analysis of the tuber crop potato.

    PubMed

    Xu, Xun; Pan, Shengkai; Cheng, Shifeng; Zhang, Bo; Mu, Desheng; Ni, Peixiang; Zhang, Gengyun; Yang, Shuang; Li, Ruiqiang; Wang, Jun; Orjeda, Gisella; Guzman, Frank; Torres, Michael; Lozano, Roberto; Ponce, Olga; Martinez, Diana; De la Cruz, Germán; Chakrabarti, S K; Patil, Virupaksh U; Skryabin, Konstantin G; Kuznetsov, Boris B; Ravin, Nikolai V; Kolganova, Tatjana V; Beletsky, Alexey V; Mardanov, Andrei V; Di Genova, Alex; Bolser, Daniel M; Martin, David M A; Li, Guangcun; Yang, Yu; Kuang, Hanhui; Hu, Qun; Xiong, Xingyao; Bishop, Gerard J; Sagredo, Boris; Mejía, Nilo; Zagorski, Wlodzimierz; Gromadka, Robert; Gawor, Jan; Szczesny, Pawel; Huang, Sanwen; Zhang, Zhonghua; Liang, Chunbo; He, Jun; Li, Ying; He, Ying; Xu, Jianfei; Zhang, Youjun; Xie, Binyan; Du, Yongchen; Qu, Dongyu; Bonierbale, Merideth; Ghislain, Marc; Herrera, Maria del Rosario; Giuliano, Giovanni; Pietrella, Marco; Perrotta, Gaetano; Facella, Paolo; O'Brien, Kimberly; Feingold, Sergio E; Barreiro, Leandro E; Massa, Gabriela A; Diambra, Luis; Whitty, Brett R; Vaillancourt, Brieanne; Lin, Haining; Massa, Alicia N; Geoffroy, Michael; Lundback, Steven; DellaPenna, Dean; Buell, C Robin; Sharma, Sanjeev Kumar; Marshall, David F; Waugh, Robbie; Bryan, Glenn J; Destefanis, Marialaura; Nagy, Istvan; Milbourne, Dan; Thomson, Susan J; Fiers, Mark; Jacobs, Jeanne M E; Nielsen, Kåre L; Sønderkær, Mads; Iovene, Marina; Torres, Giovana A; Jiang, Jiming; Veilleux, Richard E; Bachem, Christian W B; de Boer, Jan; Borm, Theo; Kloosterman, Bjorn; van Eck, Herman; Datema, Erwin; Hekkert, Bas te Lintel; Goverse, Aska; van Ham, Roeland C H J; Visser, Richard G F

    2011-07-14

    Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. PMID:21743474

  10. Complete genome sequence of Pyrolobus fumarii type strain (1AT)

    SciTech Connect

    Anderson, Iain; Goker, Markus; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, N; Pagani, Ioanna; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Huber, Harald; Yasawong, Montri; Rohde, Manfred; Spring, Stefan; Abt, Birte; Sikorski, Johannes; Wirth, Reinhard; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Pyrolobus fumarii Bl chl et al. 1997 is the type species of the genus Pyrolobus, which be- longs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106 C). This is the first com- pleted genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on Septem- ber 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley.

    PubMed

    Rostoks, Nils; Park, Yong-Jin; Ramakrishna, Wusirika; Ma, Jianxin; Druka, Arnis; Shiloff, Bryan A; SanMiguel, Phillip J; Jiang, Zeyu; Brueggeman, Robert; Sandhu, Devinder; Gill, Kulvinder; Bennetzen, Jeffrey L; Kleinhofs, Andris

    2002-05-01

    Barley (Hordeum vulgare L.) is one of the most important large-genome cereals with extensive genetic resources available in the public sector. Studies of genome organization in barley have been limited primarily to genetic markers and sparse sequence data. Here we report sequence analysis of 417.5 kb DNA from four BAC clones from different genomic locations. Sequences were analyzed with respect to gene content, the arrangement of repetitive sequences and the relationship of gene density to recombination frequencies. Gene densities ranged from 1 gene per 12 kb to 1 gene per 103 kb with an average of 1 gene per 21 kb. In general, genes were organized into islands separated by large blocks of nested retrotransposons. Single genes in apparent isolation were also found. Genes occupied 11% of the total sequence, LTR retrotransposons and other repeated elements accounted for 51.9% and the remaining 37.1% could not be annotated. PMID:12021850

  12. The complete mitochondrial genome sequence of Emperor Penguins (Aptenodytes forsteri).

    PubMed

    Xu, Qiwu; Xia, Yan; Dang, Xiao; Chen, Xiaoli

    2016-09-01

    The emperor penguin (Aptenodytes forsteri) is the largest living species of penguin. Herein, we first reported the complete mitochondrial genome of emperor penguin. The mitochondrial genome is a circular molecule of 17 301 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA, and one control region. To verify the accuracy and the utility of new determined mitogenome sequences, we constructed the species phylogenetic tree of emperor penguin together with 10 other closely species. This is the second complete mitochondrial genome of penguin, and this is going to be an important data to study mitochondrial evolution of birds. PMID:26403091

  13. A HIGH COVERAGE GENOME SEQUENCE FROM AN ARCHAIC DENISOVAN INDIVIDUAL

    PubMed Central

    Meyer, Matthias; Kircher, Martin; Gansauge, Marie-Theres; Li, Heng; Racimo, Fernando; Mallick, Swapan; Schraiber, Joshua G.; Jay, Flora; Prüfer, Kay; de Filippo, Cesare; Sudmant, Peter H.; Alkan, Can; Fu, Qiaomei; Do, Ron; Rohland, Nadin; Tandon, Arti; Siebauer, Michael; Green, Richard E.; Bryc, Katarzyna; Briggs, Adrian W.; Stenzel, Udo; Dabney, Jesse; Shendure, Jay; Kitzman, Jacob; Hammer, Michael F.; Shunkov, Michael V.; Derevianko, Anatoli P.; Patterson, Nick; Andrés, Aida M.; Eichler, Evan E.; Slatkin, Montgomery; Reich, David; Kelso, Janet; Pääbo, Svante

    2013-01-01

    We present a DNA library preparation method that has allowed us to reconstruct a high coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans. PMID:22936568

  14. The complete chloroplast genome sequence of Chloranthus japonicus.

    PubMed

    Sun, Jing; Zhang, Gang; Li, Yimin; Chen, Ying; Zhang, Xiaofei; Tang, Zhishu; Wu, Haifeng

    2016-09-01

    The complete chloroplast genome of Chloranthus japonicus, an important traditional Chinese herbal medicine, was sequenced and characterized in this study. The genome size is 158,640 bp in length with 38.9% GC content. Two inverted repeats of 26,149 bp are separated by a large single-copy region (87,724 bp) and a small single-copy region (18,618 bp). The genome contains 131 individual genes, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Eighteen genes contain one or two introns. PMID:25707409

  15. The complete chloroplast genome sequence of Curcuma flaviflora (Curcuma).

    PubMed

    Zhang, Yan; Deng, Jiabin; Li, Yangyi; Gao, Gang; Ding, Chunbang; Zhang, Li; Zhou, Yonghong; Yang, Ruiwu

    2016-09-01

    The complete chloroplast (cp) genome of Curcuma flaviflora, a medicinal plant in Southeast Asia, was sequenced. The genome size was 160 478 bp in length, with 36.3% GC content. A pair of inverted repeats (IRs) of 26 946 bp were separated by a large single copy (LSC) of 88 008 bp and a small single copy (SSC) of 18 578 bp, respectively. The cp genome contained 132 annotated genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. And 19 of these genes were duplicated in inverted repeat regions. PMID:26367332

  16. Establishing a framework for comparative analysis of genome sequences

    SciTech Connect

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  17. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

    PubMed Central

    Miller, Webb; Drautz, Daniela I.; Janecka, Jan E.; Lesk, Arthur M.; Ratan, Aakrosh; Tomsho, Lynn P.; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R.; Qi, Ji; Zhao, Fangqing; Gilbert, M. Thomas P.; Dalén, Love; Arsuaga, Juan Luis; Ericson, Per G.P.; Huson, Daniel H.; Helgen, Kristofer M.; Murphy, William J.; Götherström, Anders; Schuster, Stephan C.

    2009-01-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%–15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples’ heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes. PMID:19139089

  18. Unveiling Mycoplasma hyopneumoniae Promoters: Sequence Definition and Genomic Distribution

    PubMed Central

    Weber, Shana de Souto; Sant'Anna, Fernando Hayashi; Schrank, Irene Silveira

    2012-01-01

    Several Mycoplasma species have had their genome completely sequenced, including four strains of the swine pathogen Mycoplasma hyopneumoniae. Nevertheless, little is known about the nucleotide sequences that control transcriptional initiation in these microorganisms. Therefore, with the objective of investigating the promoter sequences of M. hyopneumoniae, 23 transcriptional start sites (TSSs) of distinct genes were mapped. A pattern that resembles the σ70 promoter −10 element was found upstream of the TSSs. However, no −35 element was distinguished. Instead, an AT-rich periodic signal was identified. About half of the experimentally defined promoters contained the motif 5′-TRTGn-3′, which was identical to the −16 element usually found in Gram-positive bacteria. The defined promoters were utilized to build position-specific scoring matrices in order to scan putative promoters upstream of all coding sequences (CDSs) in the M. hyopneumoniae genome. Two hundred and one signals were found associated with 169 CDSs. Most of these sequences were located within 100 nucleotides of the start codons. This study has shown that the number of promoter-like sequences in the M. hyopneumoniae genome is more frequent than expected by chance, indicating that most of the sequences detected are probably biologically functional. PMID:22334569

  19. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

    PubMed

    Miller, Webb; Drautz, Daniela I; Janecka, Jan E; Lesk, Arthur M; Ratan, Aakrosh; Tomsho, Lynn P; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R; Qi, Ji; Zhao, Fangqing; Gilbert, M Thomas P; Dalén, Love; Arsuaga, Juan Luis; Ericson, Per G P; Huson, Daniel H; Helgen, Kristofer M; Murphy, William J; Götherström, Anders; Schuster, Stephan C

    2009-02-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes. PMID:19139089

  20. An integrated semiconductor device enabling non-optical genome sequencing.

    PubMed

    Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James

    2011-07-21

    The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome. PMID:21776081

  1. Profiling DNA Methylomes from Microarray to Genome-Scale Sequencing

    PubMed Central

    Huang, Yi-Wen; Huang, Tim H.-M.; Wang, Li-Shu

    2010-01-01

    DNA cytosine methylation is a central epigenetic modification which plays critical roles in cellular processes including genome regulation, development and disease. Here, we review current and emerging microarray and next-generation sequencing based technologies that enhance our knowledge of DNA methylation profiling. Each methodology has limitations and their unique applications, and combinations of several modalities may help build the entire methylome. With advances on next-generation sequencing technologies, it is now possible to globally map the DNA cytosine methylation at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes. PMID:20218736

  2. Profiling DNA methylomes from microarray to genome-scale sequencing.

    PubMed

    Huang, Yi-Wei; Huang, Tim H-M; Wang, Li-Shu

    2010-04-01

    DNA cytosine methylation is a central epigenetic modification which plays critical roles in cellular processes including genome regulation, development and disease. Here, we review current and emerging microarray and next-generation sequencing based technologies that enhance our knowledge of DNA methylation profiling. Each methodology has limitations and their unique applications, and combinations of several modalities may help build the entire methylome. With advances on next-generation sequencing technologies, it is now possible to globally map the DNA cytosine methylation at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes. PMID:20218736

  3. Characteristics of cloned repeated DNA sequences in the barley genome

    SciTech Connect

    Anan'ev, E.V.; Bochkanov, S.S.; Ryzhik, M.V.; Sonina, N.V.; Chernyshev, A.I.; Shchipkova, N.I.; Yakovleva, E.Yu.

    1986-12-01

    A partial clone library of barley DNA fragments based on plasmid pBR325 was created. The cloned EcoRI-fragments of chromosomal DNA are from 2 to 14 kbp in length. More than 95% of the barley DNA inserts comprise repeated sequences of different complexity and copy number. Certain of these DNA sequences are from families comprising at least 1% of the barley genome. A significant proportion of the clones hybridize with numerous sets of restriction fragments of genome DNA and they are dispersed throughout the barley chromosomes.

  4. Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida

    PubMed Central

    Liu, Tao; Wang, Guoliang; Chi, Shan; Liu, Cui; Wang, Haiyang

    2015-01-01

    In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome. PMID:26426800

  5. Sequence modelling and an extensible data model for genomic database

    SciTech Connect

    Li, Peter Wei-Der Lawrence Berkeley Lab., CA )

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  6. Sequence modelling and an extensible data model for genomic database

    SciTech Connect

    Li, Peter Wei-Der |

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  7. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

    PubMed Central

    2011-01-01

    Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives

  8. Complete genome sequence of Thauera aminoaromatica strain MZ1T

    SciTech Connect

    Sanseverino, John; Chauhan, Archana; Lucas, Susan; Copeland, A; Lapidus, Alla L.; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Sims, David; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Chang, Yun-Juan; Larimer, Frank W; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Mikhailova, Natalia; Moser, Scott; Jegier, Patricia; Close, Dan; Wang, Ying; Layton, Alice; Allen, Michael S.; Sayler, Gary

    2012-01-01

    Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a criti-cal greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Se-quencing Program CSP{_}776774.

  9. Next Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy

    PubMed Central

    Huang, Taosheng

    2015-01-01

    This protocol is to describe the methodology to characterize mitochondria DNA (mtDNA) heteroplasmy with parallel sequencing. Mitochondria play a very important role in important cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. The mutant mtDNA and the wild type may co-exist as heteroplasmy, and cause human disease. The purpose of this methodology is to simultaneously determine mtDNA sequence and to quantify the heteroplasmy level. The protocol includes two-fragment mitochondria genome DNA PCR amplification. The PCR product is then mixed at an equimolar ratio. The samples will be barcoded and sequenced with high-throughput next-generation sequencing technology. We found that this technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree of heteroplasmic level. PMID:21975941

  10. Complete genome sequence of Allochromatium vinosum DSM 180T

    SciTech Connect

    Weissgerber, Thomas; Zigann, Renate; Bruce, David; Chang, Yun-Juan; Detter, J. Chris; Han, Cliff; Hauser, Loren John; Jeffries, Cynthia; Land, Miriam L; Munk, Christine; Tapia, Roxanne; Dahl, Christiane

    2011-01-01

    Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacte- rium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains currently five species. All members were isolated from fresh- water, brackish water or marine habitats and are predominately obligate phototrophs. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the Chromatiaceae within the purple sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp ge- nome with its 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Ge- nome Institute Community Sequencing Program.

  11. The first complete genome sequence of iris severe mosaic virus.

    PubMed

    Li, Yongqiang; Deng, Congliang; Shang, Qiaoxia; Zhao, Xiaoli; Liu, Xingliang; Zhou, Qi

    2016-04-01

    The first complete genome sequence of ISMV was determined by deep sequencing of a small RNA library constructed from ISMV-infected samples and rapid amplification of cDNA ends (RACE) PCR. The ISMV genome consists of 10,403 nucleotides excluding the poly(A) tail and contains a large open reading frame encoding a polyprotein of 3316 amino acids. Putative proteolytic cleavage sites were identified by BLAST analysis. The ISMV polyprotein showed highest amino acid sequence identity to that encoded by onion yellow dwarf virus. Phylogenetic analysis of the polyprotein amino acid sequence confirmed that ISMV forms a cluster with shallot yellow stripe virus, Cyrtanthus elatus virus A, narcissus degeneration virus and onion yellow dwarf virus. These results confirm that ISMV is a distinct member of the genus Potyvirus. PMID:26729478

  12. Mitochondrial DNA sequences in the nuclear genome of a locust.

    PubMed

    Gellissen, G; Bradfield, J Y; White, B N; Wyatt, G R

    The endosymbiotic theory of the origin of mitochondria is widely accepted, and implies that loss of genes from the mitochondria to the nucleus of eukaryotic cells has occurred over evolutionary time. However, evidence at the DNA sequence level for gene transfer between these organelles has so far been limited to a single example, the demonstration that a mitochondrial ATPase subunit gene of Neurospora crassa has an homologous partner in the nuclear genome. From a gene library of the insect, Locusta migratoria, we have now isolated two clones, representing separate fragments of nuclear DNA, which contain sequences homologous to the mitochondrial genes for ribosomal RNA, as well as regions of homology with highly repeated nuclear sequences. The results suggest the transfer of sequences between mitochondrial and nuclear genomes, followed by evolutionary divergence. PMID:6298629

  13. Complete chloroplast genome sequence of Fritillaria unibracteata var. wabuensis based on SMRT Sequencing Technology.

    PubMed

    Li, Ying; Li, Qiushi; Li, Xiwen; Song, Jingyuan; Sun, Chao

    2016-09-01

    Fritillaria unibracteata var. wabuensis is an important medicinal plant used for the treatment of cough symptoms related to the respiratory system. The chloroplast genome of F. unibracteata var. wabuensis (GenBank accession no. KF769142) was assembled using the PacBio RS platform (Pacific Biosciences, Beverly, MA) as a circle sequence with 151 009 bp. The assembled genome contains 133 genes, including 88 protein-coding, 37 tRNA, and eight rRNA genes. This genome sequence will provide important resource for further studies on the evolution of Fritillaria genus and molecular identification of Fritillaria herbs and their adulterants. This work suggests that PacBio RS is a powerful tool to sequence and assemble chloroplast genomes. PMID:26370383

  14. Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence Type 111 Pseudomonas aeruginosa Strain

    PubMed Central

    Dotson, Gabrielle A.; Dekker, John P.; Palmore, Tara N.; Segre, Julia A.

    2016-01-01

    Here, we report the draft genome sequence of a sequence type 111 Pseudomonas aeruginosa strain isolated in 2014 from a patient at the NIH Clinical Center. This P. aeruginosa strain exhibits pan-drug resistance and harbors the blaKPC-2 gene, encoding the Klebsiella pneumoniae carbapenemase enzyme, on a plasmid. PMID:26868386

  15. Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Major whole genome sequencing projects promise to identify rare and causal variants within livestock species; however, the efficient selection of animals for sequencing remains a major problem within these surveys. The goal of this project was to develop a library of high accuracy genetic variants f...

  16. Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing

    PubMed Central

    Ham, Claire; Morris, Clare

    2016-01-01

    The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays. PMID:26847885

  17. Complete mitochondrial genome sequence of Romanogobio tenuicorpus (Amur whitefin gudgeon).

    PubMed

    Dong, Fang; Tong, Guang-Xiang; Kuang, You-Yi; Sun, Xiao-Wen

    2015-01-01

    Amur whitefin gudgeon (Romanogobio tenuicorpus) belongs to the family Cyprinidae, it is freshwater aquaculture species in China. In the report, we determined the complete mitochondrial genome sequence of Romanogobio tenuicorpus, which is 16,600 bp long circular molecule with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, the conserved sequence blocks, CSB1, CSB2 and CSB3 were also detected. PMID:24409923

  18. Complete mitochondrial genome sequence of Grundulus bogotensis (Humboldt, 1821).

    PubMed

    Isaza, Juan P; Alzate, Juan F; Maldonado-Ocampo, Javier A

    2016-05-01

    The Grundulus bogotensis is an Endangered fish in Colombia. In this study, we report the complete mitochondrial DNA sequences of G. bogotensis. The entire genome comprised 17.123 bases and a GC content of 39.84%. The mitogenome sequence of G. bogotensis would contribute to better understand population genetics, and evolution of this lineage. Molecule was deposited at the GenBank database under the accession number KM677190. PMID:25405907

  19. The Genomic HyperBrowser: inferential genomics at the sequence level

    PubMed Central

    2010-01-01

    The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no. PMID:21182759

  20. Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics

    PubMed Central

    Zhao, Yue; Cottrell, Joseph; Klotzle, Brandy; Godwin, Andrew K.; Koestler, Devin; Beyerlein, Peter; Fan, Jian-Bing; Bibikova, Marina; Chien, Jeremy

    2015-01-01

    Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G > T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes. PMID:26305677

  1. Mitochondrial genome sequences and comparative genomics ofPhytophthora ramorum and P. sojae

    SciTech Connect

    Martin, Frank N.; Douda, Bensasson; Tyler, Brett M.; Boore,Jeffrey L.

    2007-01-01

    The complete sequences of the mitochondrial genomes of theoomycetes of Phytophthora ramorum and P. sojae were determined during thecourse of their complete nuclear genome sequencing (Tyler, et al. 2006).Both are circular, with sizes of 39,314 bp for P. ramorum and 42,975 bpfor P. sojae. Each contains a total of 37 identifiable protein-encodinggenes, 25 or 26 tRNAs (P. sojae and P. ramorum, respectively)specifying19 amino acids, and a variable number of ORFs (7 for P. ramorum and 12for P. sojae) which are potentially additional functional genes.Non-coding regions comprise approximately 11.5 percent and 18.4 percentof the genomes of P. ramorum and P. sojae, respectively. Relative to P.sojae, there is an inverted repeat of 1,150 bp in P. ramorum thatincludes an unassigned unique ORF, a tRNA gene, and adjacent non-codingsequences, but otherwise the gene order in both species is identical.Comparisons of these genomes with published sequences of the P. infestansmitochondrial genome reveals a number of similarities, but the gene orderin P. infestans differs in two adjacent locations due to inversions.Sequence alignments of the three genomes indicated sequence conservationranging from 75 to 85 percent and that specific regions were morevariable than others.

  2. Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

    PubMed

    Munchel, Sarah; Hoang, Yen; Zhao, Yue; Cottrell, Joseph; Klotzle, Brandy; Godwin, Andrew K; Koestler, Devin; Beyerlein, Peter; Fan, Jian-Bing; Bibikova, Marina; Chien, Jeremy

    2015-09-22

    Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C · G > T · A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes. PMID:26305677

  3. Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data

    PubMed Central

    Jang, Ho; Hur, Youngmi; Lee, Hyunju

    2016-01-01

    DNA copy number alterations (CNAs) are the main genomic events that occur during the initiation and development of cancer. Distinguishing driver aberrant regions from passenger regions, which might contain candidate target genes for cancer therapies, is an important issue. Several methods for identifying cancer-driver genes from multiple cancer patients have been developed for single nucleotide polymorphism (SNP) arrays. However, for NGS data, methods for the SNP array cannot be directly applied because of different characteristics of NGS such as higher resolutions of data without predefined probes and incorrectly mapped reads to reference genomes. In this study, we developed a wavelet-based method for identification of focal genomic alterations for sequencing data (WIFA-Seq). We applied WIFA-Seq to whole genome sequencing data from glioblastoma multiforme, ovarian serous cystadenocarcinoma and lung adenocarcinoma, and identified focal genomic alterations, which contain candidate cancer-related genes as well as previously known cancer-driver genes. PMID:27156852

  4. Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data.

    PubMed

    Jang, Ho; Hur, Youngmi; Lee, Hyunju

    2016-01-01

    DNA copy number alterations (CNAs) are the main genomic events that occur during the initiation and development of cancer. Distinguishing driver aberrant regions from passenger regions, which might contain candidate target genes for cancer therapies, is an important issue. Several methods for identifying cancer-driver genes from multiple cancer patients have been developed for single nucleotide polymorphism (SNP) arrays. However, for NGS data, methods for the SNP array cannot be directly applied because of different characteristics of NGS such as higher resolutions of data without predefined probes and incorrectly mapped reads to reference genomes. In this study, we developed a wavelet-based method for identification of focal genomic alterations for sequencing data (WIFA-Seq). We applied WIFA-Seq to whole genome sequencing data from glioblastoma multiforme, ovarian serous cystadenocarcinoma and lung adenocarcinoma, and identified focal genomic alterations, which contain candidate cancer-related genes as well as previously known cancer-driver genes. PMID:27156852

  5. 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.

  6. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes.

    PubMed

    Daniell, Henry; Lee, Seung-Bum; Grevich, Justin; Saski, Christopher; Quesada-Vargas, Tania; Guda, Chittibabu; Tomkins, Jeffrey; Jansen, Robert K

    2006-05-01

    Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf2 or ribosomal binding sites in ycf2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP, cemA, ccsA, and matK. Repeat analyses identified 33-45 direct and inverted repeats >or=30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa. It is possible that there has been a loss of conserved editing sites in potato and tomato. PMID:16575560

  7. Sequence Determination from Overlapping Fragments: A Simple Model of Whole-Genome Shotgun Sequencing

    NASA Astrophysics Data System (ADS)

    Derrida, Bernard; Fink, Thomas M.

    2002-02-01

    Assembling fragments randomly sampled from along a sequence is the basis of whole-genome shotgun sequencing, a technique used to map the DNA of the human and other genomes. We calculate the probability that a random sequence can be recovered from a collection of overlapping fragments. We provide an exact solution for an infinite alphabet and in the case of constant overlaps. For the general problem we apply two assembly strategies and give the probability that the assembly puzzle can be solved in the limit of infinitely many fragments.

  8. Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

    PubMed Central

    Chan, Yi-Chiao; Roos, Christian; Inoue-Murayama, Miho; Inoue, Eiji; Shih, Chih-Chin; Pei, Kurtis Jai-Chyi; Vigilant, Linda

    2010-01-01

    Background Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. Methodology/Principal Findings We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. Conclusions/Significance Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species. PMID:21203450

  9. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

    PubMed

    Grativol, Clícia; Regulski, Michael; Bertalan, Marcelo; McCombie, W Richard; da Silva, Felipe Rodrigues; Zerlotini Neto, Adhemar; Vicentini, Renato; Farinelli, Laurent; Hemerly, Adriana Silva; Martienssen, Robert A; Ferreira, Paulo Cavalcanti Gomes

    2014-07-01

    Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop. PMID:24773339

  10. The complete plastid genome sequence of Abies koreana (Pinaceae: Abietoideae).

    PubMed

    Yi, Dong-Keun; Yang, Jong Cheol; So, Soonku; Joo, Minjung; Kim, Dong-Kap; Shin, Chang Ho; Lee, You-Mi; Choi, Kyung

    2016-07-01

    The nucleotide sequence of the chloroplast genome from Abies koreana is the first to have complete genome sequence from genus Abies of family Pinaceae. The circular double-stranded DNA, which consists of 121,373 base pairs (bp), contains a pair of very short inverted repeat regions (IRa and IRb) of 264 bp each, which are separated by a small and large single-copy regions (SSC and LSC) of 54,197 and 66,648 bp, respectively. The genome contents of 114 genes (68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene) are similar to the chloroplast DNA of other species of Abietoideae. Loss of ndh genes was also identified in the genome of A. koreana like other genomes in the family Pinaceae. Thirteen genes contain one (11 genes) or two (rps12 and ycf3 genes) introns. In phylogenetic analysis, the tree confirms that Abies, Keteleeria and Cedrus are strongly supported as monophyletic. Other inverted repeat sequences located in 42-kb inversion points (1186 bp) include trnS-psaM-ycf12- ψtrnG genes. PMID:25812052

  11. Genome sequence and characterization of the Tsukamurella bacteriophage TPA2.

    PubMed

    Petrovski, Steve; Seviour, Robert J; Tillett, Daniel

    2011-02-01

    The formation of stable foam in activated sludge plants is a global problem for which control is difficult. These foams are often stabilized by hydrophobic mycolic acid-synthesizing Actinobacteria, among which are Tsukamurella spp. This paper describes the isolation from activated sludge of the novel double-stranded DNA phage TPA2. This polyvalent Siphoviridae family phage is lytic for most Tsukamurella species. Whole-genome sequencing reveals that the TPA2 genome is circularly permuted (61,440 bp) and that 70% of its sequence is novel. We have identified 78 putative open reading frames, 95 pairs of inverted repeats, and 6 palindromes. The TPA2 genome has a modular gene structure that shares some similarity to those of Mycobacterium phages. A number of the genes display a mosaic architecture, suggesting that the TPA2 genome has evolved at least in part from genetic recombination events. The genome sequence reveals many novel genes that should inform any future discussion on Tsukamurella phage evolution. PMID:21183635

  12. Simple repetitive sequences in the genome: structure and functional significance.

    PubMed

    Brahmachari, S K; Meera, G; Sarkar, P S; Balagurumoorthy, P; Tripathi, J; Raghavan, S; Shaligram, U; Pataskar, S

    1995-09-01

    The current explosion of DNA sequence information has generated increasing evidence for the claim that noncoding repetitive DNA sequences present within and around different genes could play an important role in genetic control processes, although the precise role and mechanism by which these sequences function are poorly understood. Several of the simple repetitive sequences which occur in a large number of loci throughout the human and other eukaryotic genomes satisfy the sequence criteria for forming non-B DNA structures in vitro. We have summarized some of the features of three different types of simple repeats that highlight the importance of repetitive DNA in the control of gene expression and chromatin organization. (i) (TG/CA)n repeats are widespread and conserved in many loci. These sequences are associated with nucleosomes of varying linker length and may play a role in chromatin organization. These Z-potential sequences can help absorb superhelical stress during transcription and aid in recombination. (ii) Human telomeric repeat (TTAGGG)n adopts a novel quadruplex structure and exhibits unusual chromatin organization. This unusual structural motif could explain chromosome pairing and stability. (iii) Intragenic amplification of (CTG)n/(CAG)n trinucleotide repeat, which is now known to be associated with several genetic disorders, could down-regulate gene expression in vivo. The overall implications of these findings vis-à-vis repetitive sequences in the genome are summarized. PMID:8582360

  13. [Genome sequencing and personalized medicine: perspectives and limitations].

    PubMed

    Le Gall, Jean-Yves; Debré, Patrice

    2014-01-01

    DNA sequencing technologies have advanced at an exponential rate in recent years: the first human genome was sequenced in 2001 after many years of effort by dozens of international laboratories at a cost of tens of millions of dollars, while in 2013 a genome can be sequenced within 24 hours for a few hundred dollars (exome sequencing takes only a few hours). More and more hospital laboratories are acquiring new high-throughput sequencing devices ("next-generation sequencers", NGS), allowing them to analyze tens or hundreds of genes, or even the entire exome. This is having a major impact on medical concepts and practices, especially with respect to genetics and oncology. This ability to search for mutations simultaneously in a large number of genes is finding applications in the diagnosis of Mendelian diseases (including at birth), routine screening for heterozygotes, and pre-conception diagnosis. NGS is now sufficiently sensitive to analyze circulating fetal DNA in maternal blood (cell-free fetal DNA, cffDNA), enabling applications such as non invasive diagnosis of fetal sex (and X-linked diseases), fetal rhesus among rhesus-negative women, trisomy and, in the near future, Mendelian mutations. Data on multifactorial diseases are still preliminary, but it should soon be possible to identify "strong" factors of genetic predisposition that have so far been beyond the scope of genome-wide association studies (GWAS). In the field of constitutional oncogenetics, NGS can also be used for simultaneous analysis of genes involved in " hereditary " cancers (21 breast cancer genes, 6 colon cancer genes, etc.). More generally, NGS can identify all genomic abnormalities (deletions, translocations, mutations) in a given malignant tissue (hemopathy or solid tumor), and has the potential to distinguish between important mutations (those that drive tumor progression) from " bystander " or accessory mutations, and also to identify "druggable" mutations amenable to targeted therapies

  14. Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

    PubMed Central

    2011-01-01

    Background Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease. Results Here we report the 18.8 Mb genome sequence of a Blastocystis subtype 7 isolate, which is the smallest stramenopile genome sequenced to date. The genome is highly compact and contains intriguing rearrangements. Comparisons with other available stramenopile genomes (plant pathogenic oomycete and diatom genomes) revealed effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer. Moreover, Blastocystis living in anaerobic conditions harbors mitochondria-like organelles. An incomplete oxidative phosphorylation chain, a partial Krebs cycle, amino acid and fatty acid metabolisms and an iron-sulfur cluster assembly are all predicted to occur in these organelles. Predicted secretory proteins possess putative activities that may alter host physiology, such as proteases, protease-inhibitors, immunophilins and glycosyltransferases. This parasite also possesses the enzymatic machinery to tolerate oxidative bursts resulting from its own metabolism or induced by the host immune system. Conclusions This study provides insights into the genome architecture of this unusual stramenopile. It also proposes candidate genes with which to study the physiopathology of this parasite and thus may lead to further investigations into Blastocystis-host interactions. PMID:21439036

  15. Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing.

    PubMed

    Belknap, William R; Wang, Yi; Huo, Naxin; Wu, Jiajie; Rockhold, David R; Gu, Yong Q; Stover, Ed

    2011-12-01

    The citrus cultivar Carrizo is the single most important rootstock to the US citrus industry and has resistance or tolerance to a number of major citrus diseases, including citrus tristeza virus, foot rot, and Huanglongbing (HLB, citrus greening). A Carrizo genomic sequence database providing approximately 3.5×genome coverage (haploid genome size approximately 367 Mb) was populated through 454 GS FLX shotgun sequencing. Analysis of the repetitive DNA fraction indicated a total interspersed repeat fraction of 36.5%. Assembly and characterization of abundant citrus Ty3/gypsy elements revealed a novel type of element containing open reading frames encoding a viral RNA-silencing suppressor protein (RNA binding protein, rbp) and a plant cytokinin riboside 5′-monophosphate phosphoribohydrolase-related protein (LONELY GUY, log). Similar gypsy elements were identified in the Populus trichocarpa genome. Gene-coding region analysis indicated that 24.4% of the nonrepetitive reads contained genic regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. The development of the Carrizo database (http://citrus.pw.usda.gov/) will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community. PMID:22133378

  16. Genome sequence of the lager brewing yeast, an interspecies hybrid.

    PubMed

    Nakao, Yoshihiro; Kanamori, Takeshi; Itoh, Takehiko; Kodama, Yukiko; Rainieri, Sandra; Nakamura, Norihisa; Shimonaga, Tomoko; Hattori, Masahira; Ashikari, Toshihiko

    2009-04-01

    This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing. The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus. Thirty-six different types of chromosomes were found including eight chromosomes with translocations between the two sub-genomes, whose breakpoints are within the orthologous open reading frames. Several gene loci responsible for typical lager brewing yeast characteristics such as maltotriose uptake and sulfite production have been increased in number by chromosomal rearrangements. Despite an overall high degree of conservation of the synteny with S. cerevisiae and S. bayanus, the syntenies were not well conserved in the sub-telomeric regions that contain lager brewing yeast characteristic and specific genes. Deletion of larger chromosomal regions, a massive unilateral decrease of the ribosomal DNA cluster and bilateral truncations of over 60 genes reflect a post-hybridization evolution process. Truncations and deletions of less efficient maltose and maltotriose uptake genes may indicate the result of adaptation to brewing. The genome sequence of this interspecies hybrid yeast provides a new tool for better understanding of lager brewing yeast behavior in industrial beer production. PMID:19261625

  17. Draft Genome Sequence of Bacillus subtilis strain KATMIRA1933

    PubMed Central

    Melnikov, Vyacheslav G.; Chikindas, Michael L.

    2014-01-01

    In this report, we present a draft sequence of Bacillus subtilis KATMIRA1933. Previous studies demonstrated probiotic properties of this strain partially attributed to production of an antibacterial compound, subtilosin. Comparative analysis of this strain’s genome with that of a commercial probiotic strain, B. subtilis Natto, is presented. PMID:24948771

  18. Genome Sequence of Ureaplasma diversum Strain ATCC 49782.

    PubMed

    Marques, Lucas M; Guimarães, Ana M S; Martins, Hellen B; Rezende, Izadora S; Barbosa, Maysa S; Campos, Guilherme B; do Nascimento, Naíla C; Dos Santos, Andrea P; Amorim, Aline T; Santos, Verena M; Messick, Joanne B; Timenetsky, Jorge

    2015-01-01

    Here, we report the complete genome sequence of Ureaplasma diversum strain ATCC 49782. This species is of bovine origin, having an association with reproductive disorders in cattle, including placentitis, fetal alveolitis, abortion, and birth of weak calves. It has a small circular chromosome of 975,425 bp. PMID:25883297

  19. Genome Sequence of a Urease-positive Campylobacter lari Strain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Campylobacter lari is frequently isolated from shore birds and can cause illness in humans. Here we report the draft whole genome sequence of an urease-positive strain of C. lari that was isolated in estuarial water on the coast of Delaware, USA....

  20. Complete Genome Sequence of Neisseria weaveri Strain NCTC13585

    PubMed Central

    Fazal, Mohammed-Abbas; Burnett, Edward; Deheer-Graham, Ana; Oliver, Karen; Holroyd, Nancy; Russell, Julie E.

    2016-01-01

    Neisseria weaveri is a commensal organism of the canine oral cavity and an occasional opportunistic human pathogen which is associated with dog bite wounds. Here we report the first complete genomic sequence of the N. weaveri NCTC13585 (CCUG30381) strain, which was originally isolated from a patient with a canine bite wound. PMID:27563039

  1. Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus.

    PubMed

    Spence, Robert J; Noune, Christopher; Hauxwell, Caroline

    2016-01-01

    Granuloviruses are widespread pathogens of Plutella xylostella L. (diamondback moth) and potential biopesticides for control of this global insect pest. We report the complete genomes of four Plutella xylostella granulovirus isolates from China, Malaysia, and Taiwan exhibiting pairs of noncoding, homologous repeat regions with significant sequence variation but equivalent length. PMID:27365355

  2. Complete Genome Sequence of Biocontrol Strain Pseudomonas fluorescens LBUM 223

    PubMed Central

    Roquigny, Roxane; Arseneault, Tanya; Gadkar, Vijay J.; Novinscak, Amy

    2015-01-01

    Pseudomonas fluorescens LBUM 223 is a plant growth-promoting rhizobacterium (PGPR) with biocontrol activity against various plant pathogens. It produces the antimicrobial metabolite phenazine-1-carboxylic acid, which is involved in the biocontrol of Streptomyces scabies, the causal agent of common scab of potato. Here, we report the complete genome sequence of P. fluorescens LBUM 223. PMID:25953163

  3. Draft Genome Sequence of Pectobacterium wasabiae Strain CFIA1002

    PubMed Central

    Yuan, Kat (Xiaoli); Adam, Zaky; Tambong, James; Lévesque, C. André; Chen, Wen; Lewis, Christopher T.; De Boer, Solke H.

    2014-01-01

    Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was recently found to cause blackleg-like symptoms on potato in the United States, Canada, and Europe. A draft genome sequence of a Canadian potato isolate of P. wasabiae CFIA1002 will enhance the characterization of its pathogenicity and host specificity features. PMID:24831134

  4. Draft Genome Sequence of Pectobacterium wasabiae Strain CFIA1002.

    PubMed

    Yuan, Kat Xiaoli; Adam, Zaky; Tambong, James; Lévesque, C André; Chen, Wen; Lewis, Christopher T; De Boer, Solke H; Li, Xiang Sean

    2014-01-01

    Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was recently found to cause blackleg-like symptoms on potato in the United States, Canada, and Europe. A draft genome sequence of a Canadian potato isolate of P. wasabiae CFIA1002 will enhance the characterization of its pathogenicity and host specificity features. PMID:24831134

  5. Len Gen: The international lentil genome sequencing project

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have been sequencing CDC Redberry using NGS of paired-end and mate-pair libraries over a wide range of sizes and technologies. The most recent draft (v0.7) of approximately 150x coverage produced scaffolds covering over half the genome (2.7 Gb of the expected 4.3 Gb). Long reads from PacBio sequ...

  6. Genome Sequences of Five Clinical Isolates of Klebsiella pneumoniae

    PubMed Central

    Lopez, L. Letti; Rusconi, Brigida; Gildersleeve, Heidi; Qi, Chao; McLaughlin, Milena; Seshu, J.

    2016-01-01

    Klebsiella pneumoniae is a nosocomial pathogen of emerging importance and displays resistance to broad-spectrum antibiotics, such as carbapenems. Here, we report the genome sequences of five clinical K. pneumoniae isolates, four of which are carbapenem resistant. Carbapenem resistance is conferred by hydrolyzing class A β-lactamases found adjacent to transposases. PMID:26966211

  7. Genome Sequences of Six Paenibacillus larvae Siphoviridae Phages.

    PubMed

    Carson, Susan; Bruff, Emily; DeFoor, William; Dums, Jacob; Groth, Adam; Hatfield, Taylor; Iyer, Aruna; Joshi, Kalyani; McAdams, Sarah; Miles, Devon; Miller, Delanie; Oufkir, Abdoullah; Raynor, Brinkley; Riley, Sara; Roland, Shelby; Rozier, Horace; Talley, Sarah; Miller, Eric S

    2015-01-01

    Six sequenced and annotated genomes of Paenibacillus larvae phages isolated from the combs of American foulbrood-diseased beehives are 37 to 45 kbp and have approximately 42% G+C content and 60 to 74 protein-coding genes. Phage Lily is most divergent from Diva, Rani, Redbud, Shelly, and Sitara. PMID:26089405

  8. Draft Genome Sequence of Chromobacterium violaceum Strain CV017

    PubMed Central

    Wang, Xiaofei; Hinshaw, Kara C.; Macdonald, Stuart J.

    2016-01-01

    We announce the draft genome sequence for Chromobacterium violaceum strain CV017, used as a model and tool to understand acyl-homoserine lactone-dependent quorum sensing. The assembly consists of 4,774,638-bp contained in 211 scaffolds. PMID:26941151

  9. Genome Sequence of an Alphabaculovirus Isolated from Choristoneura murinana

    PubMed Central

    Erlandson, Martin A.; Theilmann, David A.

    2014-01-01

    The genome sequence of a baculovirus from Choristoneura murinana is 124,689 bp, with a G+C content of 50%, and contains 148 putative open reading frames. The virus is a member of the group I alphabaculoviruses and is most closely related to several other viruses that infect Choristoneura species. PMID:24482509

  10. Draft Genome Sequence of Lactobacillus pobuzihii E100301T

    PubMed Central

    Chiu, Chi-ming; Chang, Chi-huan; Pan, Shwu-fen; Wu, Hui-chung; Li, Shiao-wen; Chang, Chuan-hsiung; Lee, Yun-shien; Chiang, Chih-ming

    2013-01-01

    Lactobacillus pobuzihii E100301T is a novel Lactobacillus species previously isolated from pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically, this strain is closest to Lactobacillus acidipiscis, but its phenotypic characteristics can be clearly distinguished from those of L. acidipiscis. We present the draft genome sequence of strain L. pobuzihii E100301T. PMID:23661478

  11. Genome Sequence of Gordonia Phage BetterKatz

    PubMed Central

    Berryman, Emily N.; Forrest, Kaitlyn M.; McHale, Lilliana; Wertz, Anthony T.; Zhuang, Zenas; Kasturiarachi, Naomi S.; Pressimone, Catherine A.; Schiebel, Johnathon G.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz’s genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages. PMID:27516497

  12. Draft Genome Sequences of Four Plant Probiotic Bacillus Strains.

    PubMed

    Jeong, Haeyoung; Park, Seung-Hwan; Choi, Soo-Keun

    2016-01-01

    Here, we report the whole-genome sequences of four Bacillus strains that exhibit plant probiotic activities. Three of them are the type strains of Bacillus endophyticus, "Bacillus gaemokensis," and Bacillus trypoxylicola, and the other, Bacillus sp. strain KCTC 13219, should be reclassified into a species belonging to the genus Lysinibacillus. PMID:27174273

  13. Complete genome sequence of Robiginitalea biformata HTCC2501.

    PubMed

    Oh, Hyun-Myung; Giovannoni, Stephen J; Lee, Kiyoung; Ferriera, Steve; Johnson, Justin; Cho, Jang-Cheon

    2009-11-01

    Robiginitalea biformata HTCC2501, isolated from the Sargasso Sea by dilution-to-extinction culturing, has been known as an aerobic chemoheterotroph with carotenoid pigments and dimorphic growth phases. Here, we announce the complete sequence of the R. biformata HTCC2501 genome, which contains genes for carotenoid biosynthesis and several macromolecule-degrading enzymes. PMID:19767438

  14. Draft Genome Sequences of the Turfgrass Pathogen Sclerotinia homoeocarpa

    PubMed Central

    Sang, Hyunkyu; Chang, Taehyun; Allan-Perkins, Elisha; Petit, Elsa

    2016-01-01

    Sclerotinia homoeocarpa (F. T. Bennett) is one of the most economically important pathogens on high-amenity cool-season turfgrasses, where it causes dollar spot. To understand the genetic mechanisms of fungicide resistance, which has become highly prevalent, the whole genomes of two isolates with varied resistance levels to fungicides were sequenced. PMID:26868400

  15. Complete Genome Sequence of Pseudomonas balearica DSM 6083T

    PubMed Central

    Salvà-Serra, Francisco; Jaén-Luchoro, Daniel; Seguí, Carolina; Aliaga, Francisco; Busquets, Antonio; Gomila, Margarita; Lalucat, Jorge

    2016-01-01

    The whole-genome sequence of Pseudomonas balearica SP1402 (DSM 6083T) has been completed and annotated. It was isolated as a naphthalene degrader from water of a lagooning wastewater treatment plant. P. balearica strains tolerate up to 8.5% NaCl and are considered true marine denitrifiers. PMID:27103708

  16. Genome Sequences of Two Lactococcus garvieae Strains Isolated from Meat

    PubMed Central

    Ferrario, Chiara; Borgo, Francesca; Eraclio, Giovanni; Fortina, Maria Grazia

    2013-01-01

    Lactococcus garvieae is an important fish pathogen and an emerging opportunistic human pathogen, as well as a component of natural microbiota in dairy and meat products. We present the first report of genome sequences of L. garvieae I113 and Tac2 strains isolated from a meat source. PMID:23405320

  17. Genome Sequence of Gordonia Phage BetterKatz.

    PubMed

    Pope, Welkin H; Berryman, Emily N; Forrest, Kaitlyn M; McHale, Lilliana; Wertz, Anthony T; Zhuang, Zenas; Kasturiarachi, Naomi S; Pressimone, Catherine A; Schiebel, Johnathon G; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz's genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages. PMID:27516497

  18. Draft Genome Sequence of the Fungus Penicillium brasilianum MG11.

    PubMed

    Horn, Fabian; Linde, Jörg; Mattern, Derek J; Walther, Grit; Guthke, Reinhard; Brakhage, Axel A; Valiante, Vito

    2015-01-01

    The genus Penicillium belongs to the phylum Ascomycota and includes a variety of fungal species important for food and drug production. We report the draft genome sequence of Penicillium brasilianum MG11. This strain was isolated from soil, and it was reported to produce different secondary metabolites. PMID:26337871

  19. Draft Genome Sequence of Rhodotorula mucilaginosa, an Emergent Opportunistic Pathogen

    PubMed Central

    Deligios, Massimo; Fraumene, Cristina; Abbondio, Marcello; Mannazzu, Ilaria; Tanca, Alessandro; Addis, Maria Filippa

    2015-01-01

    Rhodotorula mucilaginosa, a yeast with valuable biotechnological features, has also been recorded as an emergent opportunistic pathogen that might cause disease in both immunocompetent and immunocompromised individuals. Here, we report the draft genome sequence of R. mucilaginosa strain C2.5t1, which was isolated from cacao seeds in Cameroon. PMID:25858834

  20. Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus

    PubMed Central

    2016-01-01

    Granuloviruses are widespread pathogens of Plutella xylostella L. (diamondback moth) and potential biopesticides for control of this global insect pest. We report the complete genomes of four Plutella xylostella granulovirus isolates from China, Malaysia, and Taiwan exhibiting pairs of noncoding, homologous repeat regions with significant sequence variation but equivalent length. PMID:27365355