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Sample records for at-rich genomic environment

  1. OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

    PubMed Central

    Testa, Alison C.; Oliver, Richard P.; Hane, James K.

    2016-01-01

    We present a novel method to measure the local GC-content bias in genomes and a survey of published fungal species. The method, enacted as “OcculterCut” (https://sourceforge.net/projects/occultercut, last accessed April 30, 2016), identified species containing distinct AT-rich regions. In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. RIP has in turn been identified as a driver of fungal genome evolution, as RIP mutations can also occur in single-copy genes neighboring repeat-rich regions. Over time RIP perpetuates “two speeds” of gene evolution in the GC-equilibrated and AT-rich regions of fungal genomes. In this study, genomes showing evidence of this process are found to be common, particularly among the Pezizomycotina. Further analysis highlighted differences in amino acid composition and putative functions of genes from these regions, supporting the hypothesis that these regions play an important role in fungal evolution. OcculterCut can also be used to identify genes undergoing RIP-assisted diversifying selection, such as small, secreted effector proteins that mediate host-microbe disease interactions. PMID:27289099

  2. Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

    PubMed Central

    Ambrožová, Kateřina; Mandáková, Terezie; Bureš, Petr; Neumann, Pavel; Leitch, Ilia J.; Koblížková, Andrea; Macas, Jiří; Lysak, Martin A.

    2011-01-01

    Background and Aims The genus Fritillaria (Liliaceae) comprises species with extremely large genomes (1C = 30 000–127 000 Mb) and a bicontinental distribution. Most North American species (subgenus Liliorhiza) differ from Eurasian Fritillaria species by their distinct phylogenetic position and increased amounts of heterochromatin. This study examined the contribution of major repetitive elements to the genome obesity found in Fritillaria and identified repeats contributing to the heterochromatin arrays in Liliorhiza species. Methods Two Fritillaria species of similar genome size were selected for detailed analysis, one from each phylogeographical clade: F. affinis (1C = 45·6 pg, North America) and F. imperialis (1C = 43·0 pg, Eurasia). Fosmid libraries were constructed from their genomic DNAs and used for identification, sequence characterization, quantification and chromosome localization of clones containing highly repeated sequences. Key Results and Conclusions Repeats corresponding to 6·7 and 4·7 % of the F. affinis and F. imperialis genome, respectively, were identified. Chromoviruses and the Tat lineage of Ty3/gypsy group long terminal repeat retrotransposons were identified as the predominant components of the highly repeated fractions in the F. affinis and F. imperialis genomes, respectively. In addition, a heterogeneous, extremely AT-rich satellite repeat was isolated from F. affinis. The FriSAT1 repeat localized in heterochromatic bands makes up approx. 26 % of the F. affinis genome and substantial genomic fractions in several other Liliorhiza species. However, no evidence of a relationship between heterochromatin content and genome size variation was observed. Also, this study was unable to reveal any predominant repeats which tracked the increasing/decreasing trends of genome size evolution in Fritillaria. Instead, the giant Fritillaria genomes seem to be composed of many diversified families of transposable elements. We hypothesize that the

  3. Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

    PubMed Central

    Jiang, Hongying; Yi, Ming; Mu, Jianbing; Zhang, Louie; Ivens, Al; Klimczak, Leszek J; Huyen, Yentram; Stephens, Robert M; Su, Xin-zhuan

    2008-01-01

    Background Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite Plasmodium falciparum. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP) from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP) calls from the microarray with known SNP among parasite isolates. Results We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes) with high accuracy (≥ 94%) and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families) and ~18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV) among the parasites was also cataloged and compared. Conclusion A large number of mSFP were discovered from the P. falciparum genome using a high-density microarray, most of which were in clusters of highly polymorphic genes at chromosome ends. Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the P. falciparum parasite and provide useful resources for mapping important parasite traits. PMID:18724869

  4. Estimation of mutation induction rates in AT-rich sequences using a genome scanning approach after X irradiation of mouse spermatogonia.

    PubMed

    Asakawa, Jun-ichi; Nakamura, Nori; Katayama, Hiroaki; Cullings, Harry M

    2007-08-01

    We have previously used NotI as the marker enzyme (recognizing GCGGCCGC) in a genome scanning approach for detection of mutations induced in mouse spermatogonia and estimated the mutation induction rate as about 0.7 x 10(-5) per locus per Gy. To see whether different parts of the genome have different sensitivities for mutation induction, we used AflII (recognizing CTTAAG) as the marker enzyme in the present study. After the screening of 1,120 spots in each mouse offspring, we found five mutations among 92,655 spots from the unirradiated paternal genome, five mutations among 218,411 spots from the unirradiated maternal genome, and 13 mutations among 92,789 spots from 5 Gy-exposed paternal genome. Among the 23 mutations, 11 involved mouse satellite DNA sequences (AT-rich), and the remaining 12 mutations also involved AT-rich but non-satellite sequences. Both types of sequences were found as multiple, similar-sequence blocks in the genome. Counting each member of cluster mutations separately and excluding results on one hypermutable spot, the spontaneous mutation rates were estimated as 3.2 (+/- 1.9) x 10(-5) and 2.3 (+/- 1.0) x 10(-5) per locus per generation in the male and female genomes, respectively, and the mutation induction rate as 1.1 (+/- 1.2) x 10(-5) per locus per Gy. The induction rate would be reduced to 0.9 x 10(-5) per locus per Gy if satellite sequence mutations were excluded from this analysis. The results indicate that mutation induction rates do not largely differ between GC-rich and AT-rich regions: 1 x 10(-5) per locus per Gy or less, which is close to 1.08 x 10(-5) per locus per Gy, the current estimate for the mean mutation induction rate in mice.

  5. Comparative Analysis of the Mitochondrial Genomes of Callitettixini Spittlebugs (Hemiptera: Cercopidae) Confirms the Overall High Evolutionary Speed of the AT-Rich Region but Reveals the Presence of Short Conservative Elements at the Tribal Level

    PubMed Central

    Liu, Jie; Bu, Cuiping; Wipfler, Benjamin; Liang, Aiping

    2014-01-01

    The present study compares the mitochondrial genomes of five species of the spittlebug tribe Callitettixini (Hemiptera: Cercopoidea: Cercopidae) from eastern Asia. All genomes of the five species sequenced are circular double-stranded DNA molecules and range from 15,222 to 15,637 bp in length. They contain 22 tRNA genes, 13 protein coding genes (PCGs) and 2 rRNA genes and share the putative ancestral gene arrangement of insects. The PCGs show an extreme bias of nucleotide and amino acid composition. Significant differences of the substitution rates among the different genes as well as the different codon position of each PCG are revealed by the comparative evolutionary analyses. The substitution speeds of the first and second codon position of different PCGs are negatively correlated with their GC content. Among the five species, the AT-rich region features great differences in length and pattern and generally shows a 2–5 times higher substitution rate than the fastest PCG in the mitochondrial genome, atp8. Despite the significant variability in length, short conservative segments were identified in the AT-rich region within Callitettixini, although absent from the other groups of the spittlebug superfamily Cercopoidea. PMID:25285442

  6. Fungal Genomics for Energy and Environment

    SciTech Connect

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  7. [Genome, environment and plasticity of the brain underlying individual adaptation].

    PubMed

    Paunio, Tiina

    2011-01-01

    Epigenetic mechanisms mediate the interaction between environment and genome. On molecular level, these mechanisms are active in plastic processes of the brain and influence brain function and the person's ability to adapt to the environment. Genomic variations provide individual options for this adaptation, and a spectrum of behavioral patterns necessary for species preservation. Adaptation processes may also be harmful in respect of individual health, leading even to psychiatric illnesses, but are still meaningful as seen through the person's inner experience, genome or environment.

  8. Reductive Evolution of Bacterial Genome in Insect Gut Environment

    PubMed Central

    Nikoh, Naruo; Hosokawa, Takahiro; Oshima, Kenshiro; Hattori, Masahira; Fukatsu, Takema

    2011-01-01

    Obligate endocellular symbiotic bacteria of insects and other organisms generally exhibit drastic genome reduction. Recently, it was shown that symbiotic gut bacteria of some stinkbugs also have remarkably reduced genomes. Here, we report the complete genome sequence of such a gut bacterium Ishikawaella capsulata of the plataspid stinkbug Megacopta punctatissima. Gene repertoire and evolutionary patterns, including AT richness and elevated evolutionary rate, of the 745,590 bp genome were strikingly similar to those of obligate γ-proteobacterial endocellular insect symbionts like Buchnera in aphids and Wigglesworthia in tsetse flies. Ishikawaella was suggested to supply essential amino acids for the plant-sucking stinkbug as Buchnera does for the host aphid. Although Buchnera is phylogenetically closer to Wigglesworthia than to Ishikawaella, in terms of gene repertoire Buchnera was similar to Ishikawaella rather than to Wigglesworthia, providing a possible case of genome-level convergence of gene content. Meanwhile, several notable differences were identified between the genomes of Ishikawaella and Buchnera, including retention of TCA cycle genes and lack of flagellum-related genes in Ishikawaella, which may reflect their adaptation to distinct symbiotic habitats. Unexpectedly, Ishikawaella retained fewer genes related to cell wall synthesis and lipid metabolism than many endocellular insect symbionts. The plasmid of Ishikawaella encoded genes for arginine metabolism and oxalate detoxification, suggesting the possibility of additional Ishikawaella roles similar to those of human gut bacteria. Our data highlight strikingly similar evolutionary patterns that are shared between the extracellular and endocellular insect symbiont genomes. PMID:21737395

  9. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Zimmer, Carl [New York Times

    2016-07-12

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  10. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Zimmer, Carl

    2012-03-20

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  11. Explaining human uniqueness: genome interactions with environment, behaviour and culture.

    PubMed

    Varki, Ajit; Geschwind, Daniel H; Eichler, Evan E

    2008-10-01

    What makes us human? Specialists in each discipline respond through the lens of their own expertise. In fact, 'anthropogeny' (explaining the origin of humans) requires a transdisciplinary approach that eschews such barriers. Here we take a genomic and genetic perspective towards molecular variation, explore systems analysis of gene expression and discuss an organ-systems approach. Rejecting any 'genes versus environment' dichotomy, we then consider genome interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture - perhaps relaxing allowable thresholds for large-scale genomic diversity.

  12. Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models.

    PubMed

    Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A; Burgueño, Juan; Pérez-Rodríguez, Paulino; de Los Campos, Gustavo

    2017-01-05

    The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects [Formula: see text] that can be assessed by the Kronecker product of variance-covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model [Formula: see text] plus an extra component, F: , that captures random effects between environments that were not captured by the random effects [Formula: see text] We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with [Formula: see text] over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect [Formula: see text]. Copyright © 2017 Cuevas et al.

  13. Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models

    PubMed Central

    Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A.; Burgueño, Juan; Pérez-Rodríguez, Paulino; de los Campos, Gustavo

    2016-01-01

    The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects (u) that can be assessed by the Kronecker product of variance–covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model (u) plus an extra component, f, that captures random effects between environments that were not captured by the random effects u. We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with u and f over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect u. PMID:27793970

  14. Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment.

    PubMed

    Baumgartner, Michael; Roffler, Stefan; Wicker, Thomas; Pernthaler, Jakob

    2017-10-01

    Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism. Bacteria were propagated in serial batch culture in a nutrient-restricted environment either with or without a bacterivorous flagellate. Strains isolated after 26 growth cycles of the predator-prey co-cultures formed as much total biomass as the ancestor at ancestral growth conditions, albeit largely reallocated to cell aggregates. A ~273 kbp genome fragment was lost in three strains that had independently evolved with predators. These strains had significantly higher growth yield on substrate-restricted media than others that were isolated from the same treatment before the excision event. Under predation pressure, the isolates with the deletion outcompeted both, the ancestor and the strains evolved without predators even at rich growth conditions. At the same time, genome reduction led to a growth disadvantage in the presence of benzoate due to the loss of the respective degradation pathway, suggesting that niche constriction might be the price for the bidirectional optimization.

  15. Explaining human uniqueness: genome interactions with environment, behaviour and culture

    PubMed Central

    Varki, Ajit; Geschwind, Daniel H.; Eichler, Evan E.

    2009-01-01

    What makes us human? Specialists in each discipline respond through the lens of their own expertise. In fact, ‘anthropogeny’ (explaining the origin of humans) requires a transdisciplinary approach that eschews such barriers. Here we take a genomic and genetic perspective towards molecular variation, explore systems analysis of gene expression and discuss an organ-systems approach. Rejecting any ‘genes versus environment’ dichotomy, we then consider genome interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture — perhaps relaxing allowable thresholds for large-scale genomic diversity. PMID:18802414

  16. Genome-environment associations in sorghum landraces predict adaptive traits

    PubMed Central

    Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna; Deshpande, Santosh; Hash, C. Tom; Bonnette, Jason; Juenger, Thomas E.; Hyma, Katie; Acharya, Charlotte; Mitchell, Sharon E.; Buckler, Edward S.; Brenton, Zachary; Kresovich, Stephen; Morris, Geoffrey P.

    2015-01-01

    Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation. PMID:26601206

  17. Teaching "Biological Identity" as Genome/Environment Interactions

    ERIC Educational Resources Information Center

    Forissier, Thomas; Clement, Pierre

    2003-01-01

    "Biological identity" is the result of interactions between the environment and the genome. These interactions, however, were not taught before 2001. In the French syllabus for 16-year-old students, two of the five sections on genetics deal with biological identity. We analysed the texts and images of the chapters relating to these two…

  18. Teaching "Biological Identity" as Genome/Environment Interactions

    ERIC Educational Resources Information Center

    Forissier, Thomas; Clement, Pierre

    2003-01-01

    "Biological identity" is the result of interactions between the environment and the genome. These interactions, however, were not taught before 2001. In the French syllabus for 16-year-old students, two of the five sections on genetics deal with biological identity. We analysed the texts and images of the chapters relating to these two…

  19. Genomics and Metagenomics of Extreme Acidophiles in Biomining Environments

    NASA Astrophysics Data System (ADS)

    Holmes, D. S.

    2015-12-01

    Over 160 draft or complete genomes of extreme acidophiles (pH < 3) have been published, many of which are from bioleaching and other biomining environments, or are closely related to such microorganisms. In addition, there are over 20 metagenomic studies of such environments. This provides a rich source of latent data that can be exploited for understanding the biology of biomining environments and for advancing biotechnological applications. Genomic and metagenomic data are already yielding valuable insights into cellular processes, including carbon and nitrogen management, heavy metal and acid resistance, iron and sulfur oxido-reduction, linking biogeochemical processes to organismal physiology. The data also allow the construction of useful models of the ecophysiology of biomining environments and provide insight into the gene and genome evolution of extreme acidophiles. Additionally, since most of these acidophiles are also chemoautolithotrophs that use minerals as energy sources or electron sinks, their genomes can be plundered for clues about the evolution of cellular metabolism and bioenergetic pathways during the Archaean abiotic/biotic transition on early Earth. Acknowledgements: Fondecyt 1130683.

  20. Genomic Selection in Multi-environment Crop Trials

    PubMed Central

    Oakey, Helena; Cullis, Brian; Thompson, Robin; Comadran, Jordi; Halpin, Claire; Waugh, Robbie

    2016-01-01

    Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers. PMID:26976443

  1. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Rieseberg, Loren [University of British Columbia

    2016-07-12

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  2. Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Bermingham, Eldredge

    2013-03-27

    Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  3. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    ScienceCinema

    Goldberg, Robert [UCLA

    2016-07-12

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  4. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Rieseberg, Loren

    2012-03-21

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  5. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    SciTech Connect

    Goldberg, Robert

    2012-03-21

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  6. Camelid genomes reveal evolution and adaptation to desert environments.

    PubMed

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-10-21

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

  7. Genome-to-Watershed Predictive Understanding of Terrestrial Environments

    NASA Astrophysics Data System (ADS)

    Hubbard, S. S.; Agarwal, D.; Banfield, J. F.; Beller, H. R.; Brodie, E.; Long, P.; Nico, P. S.; Steefel, C. I.; Tokunaga, T. K.; Williams, K. H.

    2014-12-01

    Although terrestrial environments play a critical role in cycling water, greenhouse gasses, and other life-critical elements, the complexity of interactions among component microbes, plants, minerals, migrating fluids and dissolved constituents hinders predictive understanding of system behavior. The 'Sustainable Systems 2.0' project is developing genome-to-watershed scale predictive capabilities to quantify how the microbiome affects biogeochemical watershed functioning, how watershed-scale hydro-biogeochemical processes affect microbial functioning, and how these interactions co-evolve with climate and land-use changes. Development of such predictive capabilities is critical for guiding the optimal management of water resources, contaminant remediation, carbon stabilization, and agricultural sustainability - now and with global change. Initial investigations are focused on floodplains in the Colorado River Basin, and include iterative model development, experiments and observations with an early emphasis on subsurface aspects. Field experiments include local-scale experiments at Rifle CO to quantify spatiotemporal metabolic and geochemical responses to O2and nitrate amendments as well as floodplain-scale monitoring to quantify genomic and biogeochemical response to natural hydrological perturbations. Information obtained from such experiments are represented within GEWaSC, a Genome-Enabled Watershed Simulation Capability, which is being developed to allow mechanistic interrogation of how genomic information stored in a subsurface microbiome affects biogeochemical cycling. This presentation will describe the genome-to-watershed scale approach as well as early highlights associated with the project. Highlights include: first insights into the diversity of the subsurface microbiome and metabolic roles of organisms involved in subsurface nitrogen, sulfur and hydrogen and carbon cycling; the extreme variability of subsurface DOC and hydrological controls on carbon and

  8. Coherent synthesis of genomic associations with phenotypes and home environments.

    PubMed

    Lasky, Jesse R; Forester, Brenna R; Reimherr, Matthew

    2017-09-01

    Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome-environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade-offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis. © 2017 John Wiley & Sons Ltd.

  9. Genomic Prediction of Genotype × Environment Interaction Kernel Regression Models.

    PubMed

    Cuevas, Jaime; Crossa, José; Soberanis, Víctor; Pérez-Elizalde, Sergio; Pérez-Rodríguez, Paulino; Campos, Gustavo de Los; Montesinos-López, O A; Burgueño, Juan

    2016-11-01

    In genomic selection (GS), genotype × environment interaction (G × E) can be modeled by a marker × environment interaction (M × E). The G × E may be modeled through a linear kernel or a nonlinear (Gaussian) kernel. In this study, we propose using two nonlinear Gaussian kernels: the reproducing kernel Hilbert space with kernel averaging (RKHS KA) and the Gaussian kernel with the bandwidth estimated through an empirical Bayesian method (RKHS EB). We performed single-environment analyses and extended to account for G × E interaction (GBLUP-G × E, RKHS KA-G × E and RKHS EB-G × E) in wheat ( L.) and maize ( L.) data sets. For single-environment analyses of wheat and maize data sets, RKHS EB and RKHS KA had higher prediction accuracy than GBLUP for all environments. For the wheat data, the RKHS KA-G × E and RKHS EB-G × E models did show up to 60 to 68% superiority over the corresponding single environment for pairs of environments with positive correlations. For the wheat data set, the models with Gaussian kernels had accuracies up to 17% higher than that of GBLUP-G × E. For the maize data set, the prediction accuracy of RKHS EB-G × E and RKHS KA-G × E was, on average, 5 to 6% higher than that of GBLUP-G × E. The superiority of the Gaussian kernel models over the linear kernel is due to more flexible kernels that accounts for small, more complex marker main effects and marker-specific interaction effects.

  10. Deciphering Genome-Environment-Wide Interactions Using Exposed Subjects Only

    PubMed Central

    Zhao, Lue Ping; Fan, Wenhong; Goodman, Gary; Radich, Jerry; Martin, Paul

    2015-01-01

    The recent successes of genome-wide association studies (GWAS) have renewed interest in genome-environment-wide interaction studies (GEWIS) to discover genetic factors that modulate penetrance of environmental exposures to human diseases. Indeed, gene-environment interactions (GxE), which have not been emphasized in the GWAS era, could be a source contributing to the missing heritability, a major bottleneck limiting continuing GWAS successes. In this manuscript, we describe a design and analytic strategy to focus on GxE using only exposed subjects, dubbed as e-GEWIS. Operationally, an e-GEWIS analysis is equivalent to a GWAS analysis on exposed subjects only, and it has actually been used in some earlier GWAS without being explicitly identified as such. Through both analytics and simulations, e-GEWIS have been shown better efficiency than the usual cross-product-based analysis of GxE interaction with both cases and controls (cc-GEWIS), and they have comparable efficiency to case-only analysis of GxE (c-GEWIS), with potentially smaller sample sizes. The formalization of e-GEWIS here provides a theoretical basis to legitimize this framework for routine investigation of GxE, for more efficient GxE study designs, and for improvement of reproducibility in replicating GEWIS findings. As an illustration, we apply e-GEWIS to a lung cancer GWAS dataset to perform a GEWIS, focusing on gene and smoking interaction. The e-GEWIS analysis successfully uncovered positive genetic associations on chromosome 15 among current smokers, suggesting a gene-smoking interaction. While this signal was detected earlier, the current finding here serves as a positive control in support of this e-GEWIS strategy. PMID:25694100

  11. Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase.

    PubMed

    Lamberte, Lisa E; Baniulyte, Gabriele; Singh, Shivani S; Stringer, Anne M; Bonocora, Richard P; Stracy, Mathew; Kapanidis, Achillefs N; Wade, Joseph T; Grainger, David C

    2017-01-09

    Horizontal gene transfer permits rapid dissemination of genetic elements between individuals in bacterial populations. Transmitted DNA sequences may encode favourable traits. However, if the acquired DNA has an atypical base composition, it can reduce host fitness. Consequently, bacteria have evolved strategies to minimize the harmful effects of foreign genes. Most notably, xenogeneic silencing proteins bind incoming DNA that has a higher AT content than the host genome. An enduring question has been why such sequences are deleterious. Here, we showed that the toxicity of AT-rich DNA in Escherichia coli frequently results from constitutive transcription initiation within the coding regions of genes. Left unchecked, this causes titration of RNA polymerase and a global downshift in host gene expression. Accordingly, a mutation in RNA polymerase that diminished the impact of AT-rich DNA on host fitness reduced transcription from constitutive, but not activator-dependent, promoters.

  12. 76 FR 38399 - Assessing the Current Research, Policy, and Practice Environment in Public Health Genomics

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-30

    ... Practice Environment in Public Health Genomics AGENCY: Centers for Disease Control and Prevention (CDC... public health genomics. HHS/CDC is currently leading a process to assess the most important steps for public health genomics in the next five years. DATES: Electronic or written comments must be received on...

  13. Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses.

    PubMed

    Weber, K Scott; Jensen, Jamie L; Johnson, Steven M

    2015-01-01

    An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.

  14. Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses

    PubMed Central

    Weber, K. Scott; Jensen, Jamie L.; Johnson, Steven M.

    2015-01-01

    An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education. PMID:26241308

  15. Large-scale parallel genome assembler over cloud computing environment.

    PubMed

    Das, Arghya Kusum; Koppa, Praveen Kumar; Goswami, Sayan; Platania, Richard; Park, Seung-Jong

    2017-06-01

    The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

  16. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.

    PubMed

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.

  17. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

    PubMed Central

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

  18. Exploration of plant genomes in the FLAGdb++ environment

    PubMed Central

    2011-01-01

    Background In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). Conclusion Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features. PMID:21447150

  19. Genome Island: A Virtual Science Environment in Second Life

    ERIC Educational Resources Information Center

    Clark, Mary Anne

    2009-01-01

    Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…

  20. Genome Island: A Virtual Science Environment in Second Life

    ERIC Educational Resources Information Center

    Clark, Mary Anne

    2009-01-01

    Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…

  1. FLAGdb(++): A Bioinformatic Environment to Study and Compare Plant Genomes.

    PubMed

    Tamby, Jean Philippe; Brunaud, Véronique

    2017-01-01

    Today, the growing knowledge and data accumulation on plant genomes do not solve in a simple way the task of gene function inference. Because data of different types are coming from various sources, we need to integrate and analyze them to help biologists in this task. We created FLAGdb(++) ( http://tools.ips2.u-psud.fr/FLAGdb ) to take up this challenge for a selection of plant genomes. In order to enrich gene function predictions, structural and functional annotations of the genomes are explored to generate meta-data and to compare them. Since data are numerous and complex, we focused on accessibility and visualization with an original and user-friendly interface. In this chapter we present the main tools of FLAGdb(++) and a use-case to explore a gene family: structural and functional properties of this family and research of orthologous genes in the other plant genomes.

  2. A Novel Type Pathway-Specific Regulator and Dynamic Genome Environments of a Solanapyrone Biosynthesis Gene Cluster in the Fungus Ascochyta rabiei

    PubMed Central

    Kim, Wonyong; Park, Jeong-Jin; Gang, David R.; Peever, Tobin L.

    2015-01-01

    Secondary metabolite genes are often clustered together and situated in particular genomic regions, like the subtelomere, that can facilitate niche adaptation in fungi. Solanapyrones are toxic secondary metabolites produced by fungi occupying different ecological niches. Full-genome sequencing of the ascomycete Ascochyta rabiei revealed a solanapyrone biosynthesis gene cluster embedded in an AT-rich region proximal to a telomere end and surrounded by Tc1/Mariner-type transposable elements. The highly AT-rich environment of the solanapyrone cluster is likely the product of repeat-induced point mutations. Several secondary metabolism-related genes were found in the flanking regions of the solanapyrone cluster. Although the solanapyrone cluster appears to be resistant to repeat-induced point mutations, a P450 monooxygenase gene adjacent to the cluster has been degraded by such mutations. Among the six solanapyrone cluster genes (sol1 to sol6), sol4 encodes a novel type of Zn(II)2Cys6 zinc cluster transcription factor. Deletion of sol4 resulted in the complete loss of solanapyrone production but did not compromise growth, sporulation, or virulence. Gene expression studies with the sol4 deletion and sol4-overexpressing mutants delimited the boundaries of the solanapyrone gene cluster and revealed that sol4 is likely a specific regulator of solanapyrone biosynthesis and appears to be necessary and sufficient for induction of the solanapyrone cluster genes. Despite the dynamic surrounding genomic regions, the solanapyrone gene cluster has maintained its integrity, suggesting important roles of solanapyrones in fungal biology. PMID:26342019

  3. Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model

    USDA-ARS?s Scientific Manuscript database

    Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates for selection. Originally these models were developed without considering genotype ' environment interaction (GE). Several authors have proposed extensions of the cannonical GS model that accomm...

  4. The Challenges and Opportunities for Extending Plant Genomics to Climate (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Weston, David

    2013-03-01

    David Weston of Oak Ridge National Laboratory on "The challenges and opportunities for extending plant genomics to climate" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  5. New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Schmutz, Jeremy

    2013-03-01

    Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on "New approaches and technologies to sequence de novo plant reference genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  6. The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    ScienceCinema

    Banks, Jody [Purdue University

    2016-07-12

    Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  7. The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    SciTech Connect

    Banks, Jody

    2012-03-21

    Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  8. Genomic Analysis of Natural Variation for Seed and Plant Size in Maize ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Kaeppler, Shawn [University of Wisconsin, Madison

    2016-07-12

    Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  9. Genomic Analysis of Natural Variation for Seed and Plant Size in Maize ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Kaeppler, Shawn

    2012-03-21

    Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  10. Draft Genome Sequence of Microcystis aeruginosa CACIAM 03, a Cyanobacterium Isolated from an Amazonian Freshwater Environment

    PubMed Central

    Castro, Wendel Oliveira; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Aguiar, Délia Cristina Figueira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Fuzii, Hellen Thais; de Lima, Clayton Pereira Silva; Vianez-Júnior, João Lídio Silva Gonçalves; Nunes, Márcio Roberto Teixeira; Dall'Agnol, Leonardo Teixeira

    2016-01-01

    Given its toxigenic potential, Microcystis aeruginosa is an important bloom-forming cyanobacterium. Here, we present a draft genome and annotation of the strain CACIAM 03, which was isolated from an Amazonian freshwater environment. PMID:27856592

  11. Genomic insights into adaptation to high-altitude environments

    PubMed Central

    Cheviron, Z A; Brumfield, R T

    2012-01-01

    Elucidating the molecular genetic basis of adaptive traits is a central goal of evolutionary genetics. The cold, hypoxic conditions of high-altitude habitats impose severe metabolic demands on endothermic vertebrates, and understanding how high-altitude endotherms cope with the combined effects of hypoxia and cold can provide important insights into the process of adaptive evolution. The physiological responses to high-altitude stress have been the subject of over a century of research, and recent advances in genomic technologies have opened up exciting opportunities to explore the molecular genetic basis of adaptive physiological traits. Here, we review recent literature on the use of genomic approaches to study adaptation to high-altitude hypoxia in terrestrial vertebrates, and explore opportunities provided by newly developed technologies to address unanswered questions in high-altitude adaptation at a genomic scale. PMID:21934702

  12. The genomics of microbial domestication in the fermented food environment.

    PubMed

    Gibbons, John G; Rinker, David C

    2015-12-01

    Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.

  13. The Genomics of Microbial Domestication in the Fermented Food Environment

    PubMed Central

    Gibbons, John G; Rinker, David C

    2015-01-01

    Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were likely the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities. PMID:26338497

  14. Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Benner, Stephen [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology

    2016-07-12

    Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  15. Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Benner, Stephen

    2012-03-22

    Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  16. A Post-Genomic View of Behavioral Development and Adaptation to the Environment

    ERIC Educational Resources Information Center

    LaFreniere, Peter; MacDonald, Kevin

    2013-01-01

    Recent advances in molecular genetics and epigenetics are reviewed that have major implications for the bio-behavioral sciences and for understanding how organisms adapt to their environments at both phylogenetic and ontogenic levels. From a post-genomics perspective, the environment is as crucial as the DNA sequence for constructing the…

  17. A Post-Genomic View of Behavioral Development and Adaptation to the Environment

    ERIC Educational Resources Information Center

    LaFreniere, Peter; MacDonald, Kevin

    2013-01-01

    Recent advances in molecular genetics and epigenetics are reviewed that have major implications for the bio-behavioral sciences and for understanding how organisms adapt to their environments at both phylogenetic and ontogenic levels. From a post-genomics perspective, the environment is as crucial as the DNA sequence for constructing the…

  18. Multiplex genomic walking: Integration of the wet lab and computer lab into a single prototyping environment

    SciTech Connect

    Gillevet, P.M.

    1993-12-31

    The authors are presently sequencing the entire genome of Mycoplasma capricolum, one of the smallest of free living organisms by a Multiplex Genomic Walking strategy. This technique involves the repetitive hybridization of sequencing membranes with oligonucleotide probes to acquire sequence data in discrete steps along the genome. The technique allows one to walk a genome in a directed manner eliminating the problems associated with random shotgun assembly. Furthermore, the repetitive stripping and hybridization process is relatively simple to reproduce and has the potential to be easily automated. The Genetic Data Environment (GDE), an X Windows based Graphic User Interface has allowed the seamless integration of a core multiple sequence editor with pre-existing external sequence analysis programs and internally developed programs into a single prototypic environment. This system has facilitated linkage of the 9 Harvard Genome Lab`s internal database and automated data control systems into one Graphic User Interface which can handle the archiving and analysis of both random fluorescent sequencing data and genomic walking data from the Mycoplasma project. Finally, it has facilitated the integration of the Genomic sequence data into a PROLOG database environment for the comparative analysis of Mycoplasma capricolum and other organisms.

  19. Comparative genomic and morphological analyses of Listeria phages isolated from farm environments.

    PubMed

    Denes, Thomas; Vongkamjan, Kitiya; Ackermann, Hans-Wolfgang; Moreno Switt, Andrea I; Wiedmann, Martin; den Bakker, Henk C

    2014-08-01

    The genus Listeria is ubiquitous in the environment and includes the globally important food-borne pathogen Listeria monocytogenes. While the genomic diversity of Listeria has been well studied, considerably less is known about the genomic and morphological diversity of Listeria bacteriophages. In this study, we sequenced and analyzed the genomes of 14 Listeria phages isolated mostly from New York dairy farm environments as well as one related Enterococcus faecalis phage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. These Listeria phages, based on gene orthology and morphology, together with previously sequenced Listeria phages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large genome (~135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (~66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) of E. faecalis phages, with medium-sized genomes (~56 kb), was identified, which grouped together and shares morphological features with the novel Listeria phage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.

  20. Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

    PubMed Central

    Denes, Thomas; Ackermann, Hans-Wolfgang; Moreno Switt, Andrea I.; Wiedmann, Martin; den Bakker, Henk C.

    2014-01-01

    The genus Listeria is ubiquitous in the environment and includes the globally important food-borne pathogen Listeria monocytogenes. While the genomic diversity of Listeria has been well studied, considerably less is known about the genomic and morphological diversity of Listeria bacteriophages. In this study, we sequenced and analyzed the genomes of 14 Listeria phages isolated mostly from New York dairy farm environments as well as one related Enterococcus faecalis phage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. These Listeria phages, based on gene orthology and morphology, together with previously sequenced Listeria phages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large-genome (∼135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (∼66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) of E. faecalis phages, with medium-sized genomes (∼56 kb), was identified, which grouped together and shares morphological features with the novel Listeria phage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes. PMID:24837381

  1. Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

    SciTech Connect

    Shen, Aimee; Higgins, Darren E.; Panne, Daniel

    2009-07-22

    The MogR transcriptional repressor of the intracellular pathogen Listeria monocytogenes recognizes AT-rich binding sites in promoters of flagellar genes to downregulate flagellar gene expression during infection. We describe here the 1.8 A resolution crystal structure of MogR bound to the recognition sequence 5' ATTTTTTAAAAAAAT 3' present within the flaA promoter region. Our structure shows that MogR binds as a dimer. Each half-site is recognized in the major groove by a helix-turn-helix motif and in the minor groove by a loop from the symmetry-related molecule, resulting in a 'crossover' binding mode. This oversampling through minor groove interactions is important for specificity. The MogR binding site has structural features of A-tract DNA and is bent by approximately 52 degrees away from the dimer. The structure explains how MogR achieves binding specificity in the AT-rich genome of L. monocytogenes and explains the evolutionary conservation of A-tract sequence elements within promoter regions of MogR-regulated flagellar genes.

  2. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments.

    PubMed

    Bentkowski, Piotr; Van Oosterhout, Cock; Mock, Thomas

    2015-08-04

    Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt.

  3. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments

    PubMed Central

    Bentkowski, Piotr; Van Oosterhout, Cock; Mock, Thomas

    2015-01-01

    Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt. PMID:26242601

  4. The Plastid Genome of Najas flexilis: Adaptation to Submersed Environments Is Accompanied by the Complete Loss of the NDH Complex in an Aquatic Angiosperm

    PubMed Central

    Peredo, Elena L.; King, Ursula M.; Les, Donald H.

    2013-01-01

    The re-colonization of aquatic habitats by angiosperms has presented a difficult challenge to plants whose long evolutionary history primarily reflects adaptations to terrestrial conditions. Many aquatics must complete vital stages of their life cycle on the water surface by means of floating or emergent leaves and flowers. Only a few species, mainly within the order Alismatales, are able to complete all aspects of their life cycle including pollination, entirely underwater. Water-pollinated Alismatales include seagrasses and water nymphs (Najas), the latter being the only freshwater genus in the family Hydrocharitaceae with subsurface water-pollination. We have determined the complete nucleotide sequence of the plastid genome of Najas flexilis. The plastid genome of N. flexilis is a circular AT-rich DNA molecule of 156 kb, which displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) from the small single copy (SSC) regions. In N. flexilis, as in other Alismatales, the rps19 and trnH genes are localized in the LSC region instead of within the IR regions as in other monocots. However, the N. flexilis plastid genome presents some anomalous modifications. The size of the SSC region is only one third of that reported for closely related species. The number of genes in the plastid is considerably less. Both features are due to loss of the eleven ndh genes in the Najas flexilis plastid. In angiosperms, the absence of ndh genes has been related mainly to the loss of photosynthetic function in parasitic plants. The ndh genes encode the NAD(P)H dehydrogenase complex, believed essential in terrestrial environments, where it increases photosynthetic efficiency in variable light intensities. The modified structure of the N. flexilis plastid genome suggests that adaptation to submersed environments, where light is scarce, has involved the loss of the NDH complex in at least some photosynthetic angiosperms. PMID:23861923

  5. The plastid genome of Najas flexilis: adaptation to submersed environments is accompanied by the complete loss of the NDH complex in an aquatic angiosperm.

    PubMed

    Peredo, Elena L; King, Ursula M; Les, Donald H

    2013-01-01

    The re-colonization of aquatic habitats by angiosperms has presented a difficult challenge to plants whose long evolutionary history primarily reflects adaptations to terrestrial conditions. Many aquatics must complete vital stages of their life cycle on the water surface by means of floating or emergent leaves and flowers. Only a few species, mainly within the order Alismatales, are able to complete all aspects of their life cycle including pollination, entirely underwater. Water-pollinated Alismatales include seagrasses and water nymphs (Najas), the latter being the only freshwater genus in the family Hydrocharitaceae with subsurface water-pollination. We have determined the complete nucleotide sequence of the plastid genome of Najas flexilis. The plastid genome of N. flexilis is a circular AT-rich DNA molecule of 156 kb, which displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) from the small single copy (SSC) regions. In N. flexilis, as in other Alismatales, the rps19 and trnH genes are localized in the LSC region instead of within the IR regions as in other monocots. However, the N. flexilis plastid genome presents some anomalous modifications. The size of the SSC region is only one third of that reported for closely related species. The number of genes in the plastid is considerably less. Both features are due to loss of the eleven ndh genes in the Najas flexilis plastid. In angiosperms, the absence of ndh genes has been related mainly to the loss of photosynthetic function in parasitic plants. The ndh genes encode the NAD(P)H dehydrogenase complex, believed essential in terrestrial environments, where it increases photosynthetic efficiency in variable light intensities. The modified structure of the N. flexilis plastid genome suggests that adaptation to submersed environments, where light is scarce, has involved the loss of the NDH complex in at least some photosynthetic angiosperms.

  6. Omics and Environmental Science Genomic Approaches With Natural Fish Populations From Polluted Environments

    PubMed Central

    Bozinovic, Goran; Oleksiak, Marjorie F.

    2010-01-01

    Transcriptomics and population genomics are two complementary genomic approaches that can be used to gain insight into pollutant effects in natural populations. Transcriptomics identify altered gene expression pathways while population genomics approaches more directly target the causative genomic polymorphisms. Neither approach is restricted to a pre-determined set of genes or loci. Instead, both approaches allow a broad overview of genomic processes. Transcriptomics and population genomic approaches have been used to explore genomic responses in populations of fish from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution. Often differences in gene expression or loci between polluted and reference populations are not conserved among polluted populations suggesting a biological complexity that we do not yet fully understand. As genomic approaches become less expensive with the advent of new sequencing and genotyping technologies, they will be more widely used in complimentary studies. However, while these genomic approaches are immensely powerful for identifying candidate gene and loci, the challenge of determining biological mechanisms that link genotypes and phenotypes remains. PMID:21072843

  7. Genome-environment associations in sorghum landraces predict adaptive traits

    USDA-ARS?s Scientific Manuscript database

    Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these ...

  8. A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.

    PubMed

    Travisany, Dante; Cortés, María Paz; Latorre, Mauricio; Di Genova, Alex; Budinich, Marko; Bobadilla-Fazzini, Roberto A; Parada, Pilar; González, Mauricio; Maass, Alejandro

    2014-11-01

    Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.

  9. Genomes in Turmoil: Frugality Drives Microbial Community Structure in Extremely Acidic Environments

    NASA Astrophysics Data System (ADS)

    Holmes, D. S.

    2016-12-01

    Extremely acidic environments (To gain insight into these issues, we have conducted deep bioinformatic analyses, including metabolic reconstruction of key assimilatory pathways, phylogenomics and network scrutiny of >160 genomes of acidophiles, including representatives from Archaea, Bacteria and Eukarya and at least ten metagenomes of acidic environments [Cardenas JP, et al. pp 179-197 in Acidophiles, eds R. Quatrini and D. B. Johnson, Caister Academic Press, UK (2016)]. Results yielded valuable insights into cellular processes, including carbon and nitrogen management and energy production, linking biogeochemical processes to organismal physiology. They also provided insight into the evolutionary forces that shape the genomic structure of members of acidophile communities. Niche partitioning can explain diversity patterns in rapidly changing acidic environments such as bioleaching heaps. However, in spatially and temporally homogeneous acidic environments genome flux appears to provide deeper insight into the composition and evolution of acidic consortia. Acidophiles have undergone genome streamlining by gene loss promoting mutual coexistence of species that exploit complementarity use of scarce resources consistent with the Black Queen hypothesis [Morris JJ et al. mBio 3: e00036-12 (2012)]. Acidophiles also have a large pool of accessory genes (the microbial super-genome) that can be accessed by horizontal gene transfer. This further promotes dependency relationships as drivers of community structure and the evolution of keystone species. Acknowledgements: Fondecyt 1130683; Basal CCTE PFB16

  10. Epigenetic Mechanisms as an Interface Between the Environment and Genome.

    PubMed

    Herceg, Zdenko

    2016-01-01

    Recent advances in epigenetics have had tremendous impact on our thinking and understanding of biological phenomena and the impact of environmental stressors on complex diseases, notably cancer. Environmental and lifestyle factors are thought to be implicated in the development of a wide range of human cancers by eliciting epigenetic changes, however, the underlying mechanisms remain poorly understood. Epigenetic mechanisms can be viewed as an interface between the genome and environmental influence, therefore aberrant epigenetic events associated with environmental stressors and factors in the cell microenvironment are likely to play an important role in the onset and progression of different human malignancies. At the cellular level, aberrant epigenetic events influence critical cellular events (such as gene expression, carcinogen detoxification, DNA repair, and cell cycle), which are further modulated by risk factor exposures and thus may define the severity/subtype of cancer. This review summarizes recent progress in our understanding of the epigenetic mechanisms through which environmental stressors and endogenous factors may promote tumor development and progression.

  11. Gene-Environment Interactions in Genome-Wide Association Studies: Current Approaches and New Directions

    PubMed Central

    Winham, Stacey J; Biernacka, Joanna M.

    2013-01-01

    Background Complex psychiatric traits have long been thought to be the result of a combination of genetic and environmental factors, and gene-environment interactions are thought to play a crucial role in behavioral phenotypes and the susceptibility and progression of psychiatric disorders. Candidate gene studies to investigate hypothesized gene-environment interactions are now fairly common in human genetic research, and with the shift towards genome-wide association studies, genome-wide gene-environment interaction studies are beginning to emerge. Methods We summarize the basic ideas behind gene-environment interaction, and provide an overview of possible study designs and traditional analysis methods in the context of genome-wide analysis. We then discuss novel approaches beyond the traditional strategy of analyzing the interaction between the environmental factor and each polymorphism individually. Results Two-step filtering approaches that reduce the number of polymorphisms tested for interactions can substantially increase the power of genome-wide gene-environment studies. New analytical methods including data-mining approaches, and gene-level and pathway-level analyses, also have the capacity to improve our understanding of how complex genetic and environmental factors interact to influence psychological and psychiatric traits. Such methods, however, have not yet been utilized much in behavioral and mental health research. Conclusions Although methods to investigate gene-environment interactions are available, there is a need for further development and extension of these methods to identify gene-environment interactions in the context of genome-wide association studies. These novel approaches need to be applied in studies of psychology and psychiatry. PMID:23808649

  12. Genomic Bayesian Prediction Model for Count Data with Genotype × Environment Interaction.

    PubMed

    Montesinos-López, Abelardo; Montesinos-López, Osval A; Crossa, José; Burgueño, Juan; Eskridge, Kent M; Falconi-Castillo, Esteban; He, Xinyao; Singh, Pawan; Cichy, Karen

    2016-05-03

    Genomic tools allow the study of the whole genome, and facilitate the study of genotype-environment combinations and their relationship with phenotype. However, most genomic prediction models developed so far are appropriate for Gaussian phenotypes. For this reason, appropriate genomic prediction models are needed for count data, since the conventional regression models used on count data with a large sample size ([Formula: see text]) and a small number of parameters (p) cannot be used for genomic-enabled prediction where the number of parameters (p) is larger than the sample size ([Formula: see text]). Here, we propose a Bayesian mixed-negative binomial (BMNB) genomic regression model for counts that takes into account genotype by environment [Formula: see text] interaction. We also provide all the full conditional distributions to implement a Gibbs sampler. We evaluated the proposed model using a simulated data set, and a real wheat data set from the International Maize and Wheat Improvement Center (CIMMYT) and collaborators. Results indicate that our BMNB model provides a viable option for analyzing count data. Copyright © 2016 Montesinos-López et al.

  13. Genomic Bayesian Prediction Model for Count Data with Genotype × Environment Interaction

    PubMed Central

    Montesinos-López, Abelardo; Montesinos-López, Osval A.; Crossa, José; Burgueño, Juan; Eskridge, Kent M.; Falconi-Castillo, Esteban; He, Xinyao; Singh, Pawan; Cichy, Karen

    2016-01-01

    Genomic tools allow the study of the whole genome, and facilitate the study of genotype-environment combinations and their relationship with phenotype. However, most genomic prediction models developed so far are appropriate for Gaussian phenotypes. For this reason, appropriate genomic prediction models are needed for count data, since the conventional regression models used on count data with a large sample size (nT) and a small number of parameters (p) cannot be used for genomic-enabled prediction where the number of parameters (p) is larger than the sample size (nT). Here, we propose a Bayesian mixed-negative binomial (BMNB) genomic regression model for counts that takes into account genotype by environment (G×E) interaction. We also provide all the full conditional distributions to implement a Gibbs sampler. We evaluated the proposed model using a simulated data set, and a real wheat data set from the International Maize and Wheat Improvement Center (CIMMYT) and collaborators. Results indicate that our BMNB model provides a viable option for analyzing count data. PMID:26921298

  14. Evolution of genomic diversity and sex at extreme environments: Fungal life under hypersaline Dead Sea stress

    PubMed Central

    Kis-Papo, Tamar; Kirzhner, Valery; Wasser, Solomon P.; Nevo, Eviatar

    2003-01-01

    We have found that genomic diversity is generally positively correlated with abiotic and biotic stress levels (1–3). However, beyond a high-threshold level of stress, the diversity declines to a few adapted genotypes. The Dead Sea is the harshest planetary hypersaline environment (340 g·liter–1 total dissolved salts, ≈10 times sea water). Hence, the Dead Sea is an excellent natural laboratory for testing the “rise and fall” pattern of genetic diversity with stress proposed in this article. Here, we examined genomic diversity of the ascomycete fungus Aspergillus versicolor from saline, nonsaline, and hypersaline Dead Sea environments. We screened the coding and noncoding genomes of A. versicolor isolates by using >600 AFLP (amplified fragment length polymorphism) markers (equal to loci). Genomic diversity was positively correlated with stress, culminating in the Dead Sea surface but dropped drastically in 50- to 280-m-deep seawater. The genomic diversity pattern paralleled the pattern of sexual reproduction of fungal species across the same southward gradient of increasing stress in Israel. This parallel may suggest that diversity and sex are intertwined intimately according to the rise and fall pattern and adaptively selected by natural selection in fungal genome evolution. Future large-scale verification in micromycetes will define further the trajectories of diversity and sex in the rise and fall pattern. PMID:14645702

  15. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

    SciTech Connect

    Wurch, Louie; Giannone, Richard J.; Belisle, Bernard S.; Swift, Carolyn; Utturkar, Sagar; Hettich, Robert L.; Reysenbach, Anna-Louise; Podar, Mircea

    2016-07-05

    Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Lastly, genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea.

  16. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

    DOE PAGES

    Wurch, Louie; Giannone, Richard J.; Belisle, Bernard S.; ...

    2016-07-05

    Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Lastly, genomic and proteomicmore » comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea.« less

  17. Landscape community genomics: understanding eco-evolutionary processes in complex environments

    USGS Publications Warehouse

    Hand, Brian K.; Lowe, Winsor H.; Kovach, Ryan P.; Muhlfeld, Clint C.; Luikart, Gordon

    2015-01-01

    Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.

  18. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment.

    PubMed

    Wurch, Louie; Giannone, Richard J; Belisle, Bernard S; Swift, Carolyn; Utturkar, Sagar; Hettich, Robert L; Reysenbach, Anna-Louise; Podar, Mircea

    2016-07-05

    Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism's physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota ('Nanopusillus acidilobi') and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of 'Nanopusillus' are among the smallest known cellular organisms (100-300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea.

  19. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.

    PubMed

    Kelley, Joanna L; Peyton, Justin T; Fiston-Lavier, Anna-Sophie; Teets, Nicholas M; Yee, Muh-Ching; Johnston, J Spencer; Bustamante, Carlos D; Lee, Richard E; Denlinger, David L

    2014-08-12

    The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment.

  20. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

    PubMed Central

    Wurch, Louie; Giannone, Richard J.; Belisle, Bernard S.; Swift, Carolyn; Utturkar, Sagar; Hettich, Robert L.; Reysenbach, Anna-Louise; Podar, Mircea

    2016-01-01

    Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism's physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi') and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus' are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea. PMID:27378076

  1. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

    PubMed Central

    Kelley, Joanna L.; Peyton, Justin T.; Fiston-Lavier, Anna-Sophie; Teets, Nicholas M.; Yee, Muh-Ching; Johnston, J. Spencer; Bustamante, Carlos D.; Lee, Richard E.; Denlinger, David L.

    2014-01-01

    The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment. PMID:25118180

  2. Rice transposable elements are characterized by various methylation environments in the genome

    PubMed Central

    Takata, Miwako; Kiyohara, Akihiro; Takasu, Atsuko; Kishima, Yuji; Ohtsubo, Hisako; Sano, Yoshio

    2007-01-01

    Background Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains. Results We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE. Conclusion Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating

  3. Draft Genome Sequence of Alkalinema sp. Strain CACIAM 70d, a Cyanobacterium Isolated from an Amazonian Freshwater Environment

    PubMed Central

    Lima, Alex Ranieri Jerônimo; Castro, Wendel de Oliveira; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Aguiar, Délia Cristina Figueira; de Lima, Clayton Pereira Silva; Vianez-Júnior, João Lídio Silva Gonçalves; Nunes, Márcio Roberto Teixeira; Dall’Agnol, Leonardo Teixeira

    2017-01-01

    ABSTRACT In order to increase the genomic data of cyanobacterial strains isolated in Brazil, we hereby present the draft genome sequence of the Alkalinema sp. strain CACIAM 70d, isolated from an Amazonian freshwater environment. This report describes the first genome available for this genus. PMID:28705982

  4. Health Consequences of the Interaction of Our Genome with Our Environment

    EPA Science Inventory

    Health Consequences Of The Interaction Of Our Genome With Our Environment DM DeMarini, US EPA, RTP, NC 27711 Our primary exposures to potentially mutagenic agents are via the air, water, soil, combustion emissions, and food. Thus, characterizing the mutations induced by these...

  5. Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments.

    PubMed

    Corretto, Erika; Antonielli, Livio; Sessitsch, Angela; Kidd, Petra; Weyens, Nele; Brader, Günter

    2015-05-14

    Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants) can play a role in mobilization processes and in the phytoextraction of HM. Here, we report the whole-genome sequences and annotation of 10 Microbacterium spp. isolated from both HM-contaminated and -noncontaminated compartments. Copyright © 2015 Corretto et al.

  6. Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus.

    PubMed

    Kenzaka, Takehiko; Yamada, Yasuhiro; Tani, Katsuji

    2014-05-15

    Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding environment of a stag beetle. The draft genome sequence indicates that strain A1 harbors many biosynthesis molecules, which have antimicrobial properties, and thus potentially eliminates the fungi by producing antifungal compounds, such as siderophores.

  7. Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus

    PubMed Central

    Kenzaka, Takehiko; Yamada, Yasuhiro

    2014-01-01

    Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding environment of a stag beetle. The draft genome sequence indicates that strain A1 harbors many biosynthesis molecules, which have antimicrobial properties, and thus potentially eliminates the fungi by producing antifungal compounds, such as siderophores. PMID:24831148

  8. Health Consequences of the Interaction of Our Genome with Our Environment

    EPA Science Inventory

    Health Consequences Of The Interaction Of Our Genome With Our Environment DM DeMarini, US EPA, RTP, NC 27711 Our primary exposures to potentially mutagenic agents are via the air, water, soil, combustion emissions, and food. Thus, characterizing the mutations induced by these...

  9. Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments

    PubMed Central

    Corretto, Erika; Antonielli, Livio; Sessitsch, Angela; Kidd, Petra; Weyens, Nele

    2015-01-01

    Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants) can play a role in mobilization processes and in the phytoextraction of HM. Here, we report the whole-genome sequences and annotation of 10 Microbacterium spp. isolated from both HM-contaminated and -noncontaminated compartments. PMID:25977426

  10. Sporadic Breast Cancer Patients' Germline DNA Exhibit an AT-Rich Microsatellite Signature

    PubMed Central

    Galindo, Cristi L.; McIver, Lauren J.; Tae, Hongseok; McCormick, John F.; Skinner, Michael A.; Hoeschele, Ina; Lewis, Cheryl M.; Minna, John D.; Boothman, David A.; Garner, Harold R.

    2011-01-01

    Using a custom CGH-like oligonucleotide array to measure the global microsatellite content in the genomes of 72 cancer, cancer-free, and high risk patient and cell line samples (56 germline DNA and 16 in tumor or tumor cell line DNA) we found a unique, reproducible, and statistically significant pattern of 18 motif-specific microsatellite families (out of 962 possible 1-6 mer repeats) in breast cancer patient germline and tumor DNA, but not in germline DNA of cancer-free volunteer controls or in breast cancer patients with BRCA1/2 mutations. These high-similarity A/T rich repetitive motifs were also more pronounced in the germlines and tumors of colon cancer tumor patients (3/6 samples) and microsatellite unstable colon cancer cell lines; however, germline DNA of sporadic breast cancer patients exhibited the largest global content shift for those motifs with extreme AT/GC ratios. These results indicate that global microsatellite variability is complex, suggest the existence of a previously unknown genomic destabilization mechanism in breast cancer patients' germline DNA, and warrant further testing of such microsatellite variability as a predictor of future breast cancer development. PMID:21319262

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

    SciTech Connect

    Reeve, Wayne

    2013-03-01

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

  12. Enacting the molecular imperative: How gene-environment interaction research links bodies and environments in the Post-Genomic Age

    PubMed Central

    Darling, Katherine Weatherford; Ackerman, Sara L.; Hiatt, Robert H.; Lee, Sandra Soo-Jin; Shim, Janet K.

    2016-01-01

    Despite a proclaimed shift from ‘nature versus nurture’ to ‘genes and environment’ paradigms within biomedical and genomic science, capturing the environment and identifying gene-environment interactions (GEIs) has remained a challenge. What does ‘the environment’ mean in the post-genomic age? In this paper, we present qualitative data from a study of 33 principal investigators funded by the U.S. National Institutes of Health to conduct etiological research on three complex diseases (cancer, cardiovascular disease and diabetes). We examine their research practices and perspectives on the environment through the concept of molecularization: the social processes and transformations through which phenomena (diseases, identities, pollution, food, racial/ethnic classifications) are re-defined in terms of their molecular components and described in the language of molecular biology. We show how GEI researchers’ expansive conceptualizations of the environment ultimately yield to the imperative to molecularize and personalize the environment. They seek to ‘go into the body’ and re-work the boundaries between bodies and environments. In the process, they create epistemic hinges to facilitate a turn from efforts to understand social and environmental exposures outside the body, to quantifying their effects inside the body. GEI researchers respond to these emergent imperatives with a mixture of excitement, ambivalence and frustration. We reflect on how GEI researchers struggle to make meaning of molecules in their work, and how they grapple with molecularization as a methodological and rhetorical imperative as well as a process transforming biomedical research practices. PMID:26994357

  13. Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas

    PubMed Central

    Freel, Kelle C.; Krueger, Martin C.; Farasin, Julien; Brochier-Armanet, Céline; Barbe, Valérie; Andrès, Jeremy; Cholley, Pierre-Etienne; Dillies, Marie-Agnès; Jagla, Bernd; Koechler, Sandrine; Leva, Yann; Magdelenat, Ghislaine; Plewniak, Frédéric; Proux, Caroline; Coppée, Jean-Yves; Bertin, Philippe N.; Heipieper, Hermann J.; Arsène-Ploetze, Florence

    2015-01-01

    Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments. PMID:26422469

  14. A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction

    PubMed Central

    Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Montesinos-López, José Cricelio; Luna-Vázquez, Francisco Javier; Salinas-Ruiz, Josafhat; Herrera-Morales, José R.; Buenrostro-Mariscal, Raymundo

    2017-01-01

    There are Bayesian and non-Bayesian genomic models that take into account G×E interactions. However, the computational cost of implementing Bayesian models is high, and becomes almost impossible when the number of genotypes, environments, and traits is very large, while, in non-Bayesian models, there are often important and unsolved convergence problems. The variational Bayes method is popular in machine learning, and, by approximating the probability distributions through optimization, it tends to be faster than Markov Chain Monte Carlo methods. For this reason, in this paper, we propose a new genomic variational Bayes version of the Bayesian genomic model with G×E using half-t priors on each standard deviation (SD) term to guarantee highly noninformative and posterior inferences that are not sensitive to the choice of hyper-parameters. We show the complete theoretical derivation of the full conditional and the variational posterior distributions, and their implementations. We used eight experimental genomic maize and wheat data sets to illustrate the new proposed variational Bayes approximation, and compared its predictions and implementation time with a standard Bayesian genomic model with G×E. Results indicated that prediction accuracies are slightly higher in the standard Bayesian model with G×E than in its variational counterpart, but, in terms of computation time, the variational Bayes genomic model with G×E is, in general, 10 times faster than the conventional Bayesian genomic model with G×E. For this reason, the proposed model may be a useful tool for researchers who need to predict and select genotypes in several environments. PMID:28391241

  15. A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction.

    PubMed

    Montesinos-López, Osval A; Montesinos-López, Abelardo; Crossa, José; Montesinos-López, José Cricelio; Luna-Vázquez, Francisco Javier; Salinas-Ruiz, Josafhat; Herrera-Morales, José R; Buenrostro-Mariscal, Raymundo

    2017-06-07

    There are Bayesian and non-Bayesian genomic models that take into account G×E interactions. However, the computational cost of implementing Bayesian models is high, and becomes almost impossible when the number of genotypes, environments, and traits is very large, while, in non-Bayesian models, there are often important and unsolved convergence problems. The variational Bayes method is popular in machine learning, and, by approximating the probability distributions through optimization, it tends to be faster than Markov Chain Monte Carlo methods. For this reason, in this paper, we propose a new genomic variational Bayes version of the Bayesian genomic model with G×E using half-t priors on each standard deviation (SD) term to guarantee highly noninformative and posterior inferences that are not sensitive to the choice of hyper-parameters. We show the complete theoretical derivation of the full conditional and the variational posterior distributions, and their implementations. We used eight experimental genomic maize and wheat data sets to illustrate the new proposed variational Bayes approximation, and compared its predictions and implementation time with a standard Bayesian genomic model with G×E. Results indicated that prediction accuracies are slightly higher in the standard Bayesian model with G×E than in its variational counterpart, but, in terms of computation time, the variational Bayes genomic model with G×E is, in general, 10 times faster than the conventional Bayesian genomic model with G×E. For this reason, the proposed model may be a useful tool for researchers who need to predict and select genotypes in several environments. Copyright © 2017 Montesinos-López et al.

  16. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments

    PubMed Central

    Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

    2016-01-01

    Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8–9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. PMID:27401233

  17. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.

    PubMed

    Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

    2016-10-01

    Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Genomic Selection Improves Response to Selection in Resilience by Exploiting Genotype by Environment Interactions

    PubMed Central

    Mulder, Han A.

    2016-01-01

    Genotype by environment interactions (GxE) are very common in livestock and hamper genetic improvement. On the other hand, GxE is a source of genetic variation: genetic variation in response to environment, e.g., environmental perturbations such as heat stress or disease. In livestock breeding, there is tendency to ignore GxE because of increased complexity of models for genetic evaluations and lack of accuracy in extreme environments. GxE, however, creates opportunities to increase resilience of animals toward environmental perturbations. The main aim of the paper is to investigate to which extent GxE can be exploited with traditional and genomic selection methods. Furthermore, we investigated the benefit of reaction norm (RN) models compared to conventional methods ignoring GxE. The questions were addressed with selection index theory. GxE was modeled according to a linear RN model in which the environmental gradient is the contemporary group mean. Economic values were based on linear and non-linear profit equations. Accuracies of environment-specific (G)EBV were highest in intermediate environments and lowest in extreme environments. RN models had higher accuracies of (G)EBV in extreme environments than conventional models ignoring GxE. Genomic selection always resulted in higher response to selection in all environments than sib or progeny testing schemes. The increase in response was with genomic selection between 9 and 140% compared to sib testing and between 11 and 114% compared to progeny testing when the reference population consisted of 1 million animals across all environments. When the aim was to decrease environmental sensitivity, the response in slope of the RN model with genomic selection was between 1.09 and 319 times larger than with sib or progeny testing and in the right direction in contrast to sib and progeny testing that still increased environmental sensitivity. This shows that genomic selection with large reference populations offers great

  19. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes

    PubMed Central

    Fang, Xiaodong; Seim, Inge; Huang, Zhiyong; Gerashchenko, Maxim V.; Xiong, Zhiqiang; Turanov, Anton A.; Zhu, Yabing; Lobanov, Alexei V.; Fan, Dingding; Yim, Sun Hee; Yao, Xiaoming; Ma, Siming; Yang, Lan; Lee, Sang-Goo; Kim, Eun Bae; Bronson, Roderick T.; Šumbera, Radim; Buffenstein, Rochelle; Zhou, Xin; Krogh, Anders; Park, Thomas J.; Zhang, Guojie; Wang, Jun; Gladyshev, Vadim N.

    2014-01-01

    SUMMARY Subterranean mammals spend their lives in dark, unventilated environments rich in carbon dioxide and ammonia, and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis) and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber). Comparative genome analysis, along with transcriptomes of related subterranean rodents, reveal candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, aberrant melatonin system, pain insensitivity, and novel processing of 28S rRNA. Together, the new genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance and longevity. PMID:25176646

  20. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI

    2016-07-12

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  1. Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Wullschleger, Stan [ORNL

    2016-07-12

    Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

  2. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    ScienceCinema

    Gmitter Jr, Fred [University of Florida

    2016-07-12

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  3. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    SciTech Connect

    Gmitter Jr, Fred

    2012-03-21

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  4. Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Wullschleger, Stan

    2012-03-22

    Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

  5. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Shih, Patrick

    2012-03-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  6. Optimization of multi-environment trials for genomic selection based on crop models.

    PubMed

    Rincent, R; Kuhn, E; Monod, H; Oury, F-X; Rousset, M; Allard, V; Le Gouis, J

    2017-08-01

    We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters. The efficiency of this approach relies on the quality of the parameter estimates, which depends on the environments composing this MET used for calibration. The objective of this study was to determine a method to optimize the set of environments composing the MET for estimating genetic parameters in this context. A criterion called OptiMET was defined to this aim, and was evaluated on simulated and real data, with the example of wheat phenology. The MET defined with OptiMET allowed estimating the genetic parameters with lower error, leading to higher QTL detection power and higher prediction accuracies. MET defined with OptiMET was on average more efficient than random MET composed of twice as many environments, in terms of quality of the parameter estimates. OptiMET is thus a valuable tool to determine optimal experimental conditions to best exploit MET and the phenotyping tools that are currently developed.

  7. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Muchero, Wellington [Oak Ridge National Laboratory

    2016-07-12

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  8. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Muchero, Wellington

    2012-03-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  9. Living with genome instability: the adaptation of phytoplasmas todiverse environments of their insect and plant hosts

    SciTech Connect

    Bai, Xiaodong; Zhang, Jianhua; Ewing, Adam; Miller, Sally A.; Radek, Agnes; Shevchenko, Dimitriy; Tsukerman, Kiryl; Walunas, Theresa; Lapidus, Alla; Campbell, John W.; Hogenhout Saskia A.

    2006-02-17

    Phytoplasmas (Candidatus Phytoplasma, Class Mollicutes) cause disease in hundreds of economically important plants, and are obligately transmitted by sap-feeding insects of the order Hemiptera, mainly leafhoppers and psyllids. The 706,569-bp chromosome and four plasmids of aster yellows phytoplasma strain witches broom (AY-WB) were sequenced and compared to the onion yellows phytoplasma strain M (OY-M) genome. The phytoplasmas have small repeat-rich genomes. The repeated DNAs are organized into large clusters, potential mobile units (PMUs), which contain tra5 insertion sequences (ISs), and specialized sigma factors and membrane proteins. So far, PMUs are unique to phytoplasmas. Compared to mycoplasmas, phytoplasmas lack several recombination and DNA modification functions, and therefore phytoplasmas probably use different mechanisms of recombination, likely involving PMUs, for the creation of variability, allowing phytoplasmas to adjust to the diverse environments of plants and insects. The irregular GC skews and presence of ISs and large repeated sequences in the AY-WB and OY-M genomes are indicative of high genomic plasticity. Nevertheless, segments of {approx}250 kb, located between genes lplA and glnQ are syntenic between the two phytoplasmas, contain the majority of the metabolic genes and no ISs. AY-WB is further along in the reductive evolution process than OY-M. The AY-WB genome is {approx}154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Further, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M. This is the first comparative phytoplasma genome analysis and report of the existence of PMUs in phytoplasma genomes.

  10. Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis.

    PubMed

    Gordon, Blair R G; Li, Yifei; Wang, Linru; Sintsova, Anna; van Bakel, Harm; Tian, Songhai; Navarre, William Wiley; Xia, Bin; Liu, Jun

    2010-03-16

    Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 of Mycobacterium tuberculosis is a unique nucleoid-associated protein that binds AT-rich regions of the genome, including genomic islands acquired by horizontal gene transfer and regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM and PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain-swapping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA-binding domain. Nuclear magnetic resonance analysis of the DNA-binding domain of Lsr2 and its interaction with DNA reveals a unique structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve a function similar to the Enterobacteriaceae H-NS, likely coordinating global gene regulation and virulence in this group of medically important bacteria.

  11. The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment

    PubMed Central

    Barton, Michael D.; Petronio, Michael; Giarrizzo, Juan G.; Bowling, Bethany V.

    2013-01-01

    Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes. PMID:23995634

  12. Increased prediction accuracy in wheat breeding trials using a marker × environment interaction genomic selection model.

    PubMed

    Lopez-Cruz, Marco; Crossa, Jose; Bonnett, David; Dreisigacker, Susanne; Poland, Jesse; Jannink, Jean-Luc; Singh, Ravi P; Autrique, Enrique; de los Campos, Gustavo

    2015-02-06

    Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates of selection. Originally, these models were developed without considering genotype × environment interaction(G×E). Several authors have proposed extensions of the single-environment GS model that accommodate G×E using either covariance functions or environmental covariates. In this study, we model G×E using a marker × environment interaction (M×E) GS model; the approach is conceptually simple and can be implemented with existing GS software. We discuss how the model can be implemented by using an explicit regression of phenotypes on markers or using co-variance structures (a genomic best linear unbiased prediction-type model). We used the M×E model to analyze three CIMMYT wheat data sets (W1, W2, and W3), where more than 1000 lines were genotyped using genotyping-by-sequencing and evaluated at CIMMYT's research station in Ciudad Obregon, Mexico, under simulated environmental conditions that covered different irrigation levels, sowing dates and planting systems. We compared the M×E model with a stratified (i.e., within-environment) analysis and with a standard (across-environment) GS model that assumes that effects are constant across environments (i.e., ignoring G×E). The prediction accuracy of the M×E model was substantially greater of that of an across-environment analysis that ignores G×E. Depending on the prediction problem, the M×E model had either similar or greater levels of prediction accuracy than the stratified analyses. The M×E model decomposes marker effects and genomic values into components that are stable across environments (main effects) and others that are environment-specific (interactions). Therefore, in principle, the interaction model could shed light over which variants have effects that are stable across environments and which ones are responsible for G×E. The data set and the scripts required to reproduce the analysis are

  13. Adaptive evolution of an artificial RNA genome to a reduced ribosome environment.

    PubMed

    Mizuuchi, Ryo; Ichihashi, Norikazu; Usui, Kimihito; Kazuta, Yasuaki; Yomo, Tetsuya

    2015-03-20

    The reconstitution of an artificial system that has the same evolutionary ability as a living thing is a major challenge in the in vitro synthetic biology. In this study, we tested the adaptive evolutionary ability of an artificial RNA genome replication system, termed the translation-coupled RNA replication (TcRR) system. In a previous work, we performed a study of the long-term evolution of the genome with an excess amount of ribosome. In this study, we continued the evolution experiment in a reduced-ribosome environment and observed that the mutant genome compensated for the reduced ribosome concentration. This result demonstrated the ability of the TcRR system to adapt and may be a step toward generating living things with evolutionary ability.

  14. Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.

    PubMed

    Ozdemir, Vural; Motulsky, Arno G; Kolker, Eugene; Godard, Béatrice

    2009-02-01

    The relationships between food, nutrition science, and health outcomes have been mapped over the past century. Genomic variation among individuals and populations is a new factor that enriches and challenges our understanding of these complex relationships. Hence, the confluence of nutritional science and genomics-nutrigenomics--was the focus of the OMICS: A Journal of Integrative Biology in December 2008 (Part 1). The 2009 Special Issue (Part 2) concludes the analysis of nutrigenomics research and innovations. Together, these two issues expand the scope and depth of critical scholarship in nutrigenomics, in keeping with an integrated multidisciplinary analysis across the bioscience, omics technology, social, ethical, intellectual property and policy dimensions. Historically, the field of pharmacogenetics provided the first examples of specifically identifiable gene variants predisposing to unexpected responses to drugs since the 1950s. Brewer coined the term ecogenetics in 1971 to broaden the concept of gene-environment interactions from drugs and nutrition to include environmental agents in general. In the mid-1990s, introduction of high-throughput technologies led to the terms pharmacogenomics, nutrigenomics and ecogenomics to describe, respectively, the contribution of genomic variability to differential responses to drugs, food, and environment defined in the broadest sense. The distinctions, if any, between these newer fields (e.g., nutrigenomics) and their predecessors (e.g., nutrigenetics) remain to be delineated. For nutrigenomics, its reliance on genome-wide analyses may lead to detection of new biological mechanisms governing host response to food. Recognizing "genome-environment interactions" as the conceptual thread that connects and runs through pharmacogenomics, nutrigenomics, and ecogenomics may contribute toward anticipatory governance and prospective real-time analysis of these omics fields. Such real-time analysis of omics technologies and

  15. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

    SciTech Connect

    Norton, Jeanette M.; Klotz, Martin G; Stein, Lisa Y; Arp, D J; Bottomley, Peter J; Chain, Patrick S. G.; Hauser, Loren John; Land, Miriam L; Larimer, Frank W; Shin, M; Starkenburg, Shawn R

    2008-01-01

    The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2827 putative proteins. Of these, 2026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presence of gene clusters encoding urease and hydrogenase, a RuBisCO-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced AOB genomes. Gene clusters encoding proteins associated with outer membrane and cell envelope functions including transporters, porins, exopolysaccharide synthesis, capsule formation and protein sorting/export were abundant. Numerous sensory transduction and response regulator gene systems directed towards sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate and cyanophycin storage and utilization were identified providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

  16. Immersive virtual environment technology: a promising tool for future social and behavioral genomics research and practice.

    PubMed

    Persky, Susan; McBride, Colleen M

    2009-12-01

    Social and behavioral research needs to get started now if scientists are to direct genomic discoveries to address pressing public health problems. Advancing social and behavioral science will require innovative and rigorous communication methodologies that move researchers beyond reliance on traditional tools and their inherent limitations. One such emerging research tool is immersive virtual environment technology (virtual reality), a methodology that gives researchers the ability to maintain high experimental control and mundane realism of scenarios; portray and manipulate complex, abstract objects and concepts; and implement innovative implicit behavioral measurement. This report suggests the role that immersive virtual environment technology can play in furthering future research in genomics-related education, decision making, test intentions, behavior change, and health-care provider behaviors. Practical implementation and challenges are also discussed.

  17. Writ large: Genomic Dissection of the Effect of Cellular Environment on Immune Response

    PubMed Central

    Yosef, Nir; Regev, Aviv

    2016-01-01

    Cells of the immune system routinely respond to cues from their local environment and feedback to their surrounding through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell state, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles, on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules, in achieving and maintaining appropriate responses to a changing environment. These provide a first step toward a systematic understanding of molecular circuits in complex tissues. PMID:27846493

  18. Writ large: Genomic dissection of the effect of cellular environment on immune response.

    PubMed

    Yosef, Nir; Regev, Aviv

    2016-10-07

    Cells of the immune system routinely respond to cues from their local environment and feed back to their surroundings through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell states, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules in achieving and maintaining appropriate responses to a changing environment. These provide a first step toward a systematic understanding of molecular circuits in complex tissues. Copyright © 2016, American Association for the Advancement of Science.

  19. Immersive Virtual Environment Technology: A Promising Tool for Future Social and Behavioral Genomics Research and Practice

    PubMed Central

    Persky, Susan; McBride, Colleen M.

    2009-01-01

    Social and behavioral research needs to get started now if we are to direct genomic discoveries to address pressing public health problems. Advancing social and behavioral science will require innovative and rigorous communication methodologies that move us beyond reliance on traditional tools and their inherent limitations. One such emerging research tool is immersive virtual environment technology (aka: virtual reality), a methodology that gives researchers the ability to maintain high experimental control and mundane realism of scenarios, portray and manipulate complex, abstract objects and concepts, and implement innovative implicit behavioral measurement. This report suggests the role that immersive virtual environment technology can play in furthering future research in genomics-related: education, decision-making, test intentions, behavior change, and healthcare provider behaviors. Practical implementation and challenges are also discussed. PMID:20183376

  20. GNARE: an environment for Grid-based high-throughput genome analysis.

    SciTech Connect

    Sulakhe, D.; Rodriguez, A.; D'Souza, M.; Wilde, M.; Nefedova, V.; Foster, I.; Maltsev, N.; Mathematics and Computer Science; Univ. of Chicago

    2005-01-01

    Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. However, applying the potentially enormous scientific value of this information to the understanding of biological systems requires computing and data storage technology of an unprecedented scale. The grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis. To leverage this we have developed the Genome Analysis Research Environment (GNARE) - a scalable computational system for the high-throughput analysis of genomes, which provides an integrated database and computational backend for data-driven bioinformatics applications. GNARE efficiently automates the major steps of genome analysis including acquisition of data from multiple genomic databases; data analysis by a diverse set of bioinformatics tools; and storage of results and annotations. High-throughput computations in GNARE are performed using distributed heterogeneous grid computing resources such as Grid2003, TeraGrid, and the DOE science grid. Multi-step genome analysis workflows involving massive data processing, the use of application-specific toots and algorithms and updating of an integrated database to provide interactive Web access to results are all expressed and controlled by a 'virtual data' model which transparently maps computational workflows to distributed grid resources. This paper describes how Grid technologies such as Globus, Condor, and the Gryphyn virtual data system were applied in the development of GNARE. It focuses on our approach to Grid resource allocation and to the use of GNARE as a computational framework for the development of bioinformatics applications.

  1. Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment

    PubMed Central

    2011-01-01

    Background Polycomb/Trithorax response elements (PREs) are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position. Results We adapted the ΦC31 site-specific integration tool to enable systematic quantitative comparison of PREs and sequence variants at identical genomic locations. In this adaptation, a miniwhite (mw) reporter in combination with eye-pigment analysis gives a quantitative readout of PRE function. We compared the Hox PRE Frontabdominal-7 (Fab-7) with a PRE from the vestigial (vg) gene at four landing sites. The analysis revealed that the Fab-7 and vg PREs have fundamentally different properties, both in terms of their interaction with the genomic environment at each site and their inherent silencing abilities. Furthermore, we used the ΦC31 tool to examine the effect of deletions and mutations in the vg PRE, identifying a 106 bp region containing a previously predicted motif (GTGT) that is essential for silencing. Conclusions This analysis showed that different PREs have quantifiably different properties, and that changes in as few as four base pairs have profound effects on PRE function, thus illustrating the power and sensitivity of ΦC31 site-specific integration as a tool for the rapid and quantitative dissection of elements of PRE design. PMID:21410956

  2. Plants from Chernobyl zone could shed light on genome stability in radioactive environment

    NASA Astrophysics Data System (ADS)

    Shevchenko, Galina; Talalaiev, Oleksandr; Doonan, John

    2016-07-01

    For nearly 30 years, despite of chronic radiation, flora in Chernobyl zone continue to flourish, evidencing the adaptation of plants to such an environment. Keeping in mind interplanetary missions, this phenomenon is a challenge for plant space research since it highlights the possible mechanisms of genome protection and stabilization in harmful environment. Plants are sessile organisms and, contrary to animals, could not escape the external impact. Therefore, plants should evolve the robust system allowing DNA-protection against damage, which is of special interest. Our investigations show that Arabidopsis thaliana from Chernobyl zone tolerate radiomimetics and heavy metals better than control plants from non-polluted areas. Besides, its genome is less affected by such mutagens. qPCR investigations have revealed up-regulation of some genes involved in DNA damage response. In particular, expression of ATR is increased slightly and downstream expression of CycB1:1 gene is increased significantly after bleomycin treatment suggesting role of ATR-dependent pathway in genome stabilization. Several DNA repair pathways are known to exist in plants. We continue investigations on gene expression from different DNA repair pathways as well as cell cycle regulation and investigation of PCD hallmarks in order to reveal the mechanism of plant tolerance to radiation environment. Our investigations provide unique information for space researchers working on biotechnology of radiation tolerant plants.

  3. Space environment induced mutations prefer to occur at polymorphic sites of rice genomes

    NASA Astrophysics Data System (ADS)

    Li, Y.; Liu, M.; Cheng, Z.; Sun, Y.

    To explore the genomic characteristics of rice mutants induced by space environment, space-induced mutants 971-5, 972-4, and R955, which acquired new traits after space flight such as increased yield, reduced resistance to rice blast, and semi-dwarfism compared with their on-ground controls, 971ck, 972ck, and Bing95-503, respectively, together with other 8 japonica and 3 indica rice varieties, 17 in total, were analyzed by amplified fragment length polymorphism (AFLP) method. We chose 16 AFLP primer-pairs which generated a total of 1251 sites, of which 745 (59.6%) were polymorphic over all the genotypes. With the 16 pairs of primer combinations, 54 space-induced mutation sites were observed in 971-5, 86 in 972-4, and 5 in R955 compared to their controls, and the mutation rates were 4.3%, 6.9% and 0.4%, respectively. Interestingly, 75.9%, 84.9% and 100% of the mutation sites identified in 971-5, 972-4, and R955 occurred in polymorphic sites. This result suggests that the space environment preferentially induced mutations at polymorphic sites in rice genomes and might share a common mechanism with other types of mutagens. It also implies that polymorphic sites in genomes are potential "hotspots" for mutations induced by the space environment.

  4. Identification of thermoacidophilic bacteria and a new Alicyclobacillus genomic species isolated from acidic environments in Japan.

    PubMed

    Goto, Keiichi; Tanimoto, Yasuhide; Tamura, Takashi; Mochida, Kaoru; Arai, Daisuke; Asahara, Mika; Suzuki, Masayuki; Tanaka, Hidehiko; Inagaki, Kenji

    2002-08-01

    Sixty strains of thermoacidophilic bacteria have been isolated from soil and water samples obtained from various acidic environments in Japan. An initial comparative sequence analysis of the hypervariable regions of the 16S rDNA revealed that all strains could be assigned to the Alicyclobacillus acidocaldarius- Alicyclobacillus genomic species 1 group, which could be further subdivided into three clusters (Clusters I-III). On the basis of phenotypic characteristics, chemotaxonomic profiles, and phylogenetic data of six selected strains, five strains were identified as either A. acidocaldarius or Alicyclobacillus genomic species 1; however, one strain (MIH 332) could not be determined to belong to either of these species. 16S rDNA sequence homology values between strain MIH 332 and the reference strains of A. acidocaldarius (ATCC 27009(T)) and Alicyclobacillus genomic species 1 (DSM 11984) were 98.8% and 99.1%, respectively, which were higher than the corresponding similarity between the reference strains (98.4%). On the other hand, DNA-DNA hybridization levels between strain MIH 332 and the reference strains were 39% and 44%, respectively, which were lower than the value between the reference strains (59% or 65%). However, the phenotype of strain MIH 332 was also similar to those of the reference strains, and a typical phenotype could not be found for the strain, thus indicating that the strain may be a new genomic species of A. acidocaldarius, for which the name Alicyclobacillus genomic species 2 is tentatively proposed. The results of this study suggest that A. acidocaldarius and its related species are widely distributed in acidic environments in Japan, with slight regional variations in morphological and genotypic characteristics.

  5. Genome analysis of Pseudoalteromonas flavipulchra JG1 reveals various survival advantages in marine environment

    PubMed Central

    2013-01-01

    Background Competition between bacteria for habitat and resources is very common in the natural environment and is considered to be a selective force for survival. Many strains of the genus Pseudoalteromonas were confirmed to produce bioactive compounds that provide those advantages over their competitors. In our previous study, P. flavipulchra JG1 was found to synthesize a Pseudoalteromonas flavipulchra antibacterial Protein (PfaP) with L-amino acid oxidase activity and five small chemical compounds, which were the main competitive agents of the strain. In addition, the genome of this bacterium has been previously sequenced as Whole Genome Shotgun project (PMID: 22740664). In this study, more extensive genomic analysis was performed to identify specific genes or gene clusters which related to its competitive feature, and further experiments were carried out to confirm the physiological roles of these genes when competing with other microorganisms in marine environment. Results The antibacterial protein PfaP may also participate in the biosynthesis of 6-bromoindolyl-3-acetic acid, indicating a synergistic effect between the antibacterial macromolecule and small molecules. Chitinases and quorum quenching enzymes present in P. flavipulchra, which coincide with great chitinase and acyl homoserine lactones degrading activities of strain JG1, suggest other potential mechanisms contribute to antibacterial/antifungal activities. Moreover, movability and rapid response mechanisms to phosphorus starvation and other stresses, such as antibiotic, oxidative and heavy metal stress, enable JG1 to adapt to deleterious, fluctuating and oligotrophic marine environments. Conclusions The genome of P. flavipulchra JG1 exhibits significant genetic advantages against other microorganisms, encoding antimicrobial agents as well as abilities to adapt to various adverse environments. Genes involved in synthesis of various antimicrobial substances enriches the antagonistic mechanisms of P

  6. Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction

    PubMed Central

    Bandeira e Sousa, Massaine; Cuevas, Jaime; de Oliveira Couto, Evellyn Giselly; Pérez-Rodríguez, Paulino; Jarquín, Diego; Fritsche-Neto, Roberto; Burgueño, Juan; Crossa, Jose

    2017-01-01

    Multi-environment trials are routinely conducted in plant breeding to select candidates for the next selection cycle. In this study, we compare the prediction accuracy of four developed genomic-enabled prediction models: (1) single-environment, main genotypic effect model (SM); (2) multi-environment, main genotypic effects model (MM); (3) multi-environment, single variance G×E deviation model (MDs); and (4) multi-environment, environment-specific variance G×E deviation model (MDe). Each of these four models were fitted using two kernel methods: a linear kernel Genomic Best Linear Unbiased Predictor, GBLUP (GB), and a nonlinear kernel Gaussian kernel (GK). The eight model-method combinations were applied to two extensive Brazilian maize data sets (HEL and USP data sets), having different numbers of maize hybrids evaluated in different environments for grain yield (GY), plant height (PH), and ear height (EH). Results show that the MDe and the MDs models fitted with the Gaussian kernel (MDe-GK, and MDs-GK) had the highest prediction accuracy. For GY in the HEL data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 9 to 32%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 9 to 49%. For GY in the USP data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 0 to 7%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 34 to 70%. For traits PH and EH, gains in prediction accuracy of models with GK compared to models with GB were smaller than those achieved in GY. Also, these gains in prediction accuracy decreased when a more difficult prediction problem was studied. PMID:28455415

  7. Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction.

    PubMed

    Bandeira E Sousa, Massaine; Cuevas, Jaime; de Oliveira Couto, Evellyn Giselly; Pérez-Rodríguez, Paulino; Jarquín, Diego; Fritsche-Neto, Roberto; Burgueño, Juan; Crossa, Jose

    2017-06-07

    Multi-environment trials are routinely conducted in plant breeding to select candidates for the next selection cycle. In this study, we compare the prediction accuracy of four developed genomic-enabled prediction models: (1) single-environment, main genotypic effect model (SM); (2) multi-environment, main genotypic effects model (MM); (3) multi-environment, single variance G×E deviation model (MDs); and (4) multi-environment, environment-specific variance G×E deviation model (MDe). Each of these four models were fitted using two kernel methods: a linear kernel Genomic Best Linear Unbiased Predictor, GBLUP (GB), and a nonlinear kernel Gaussian kernel (GK). The eight model-method combinations were applied to two extensive Brazilian maize data sets (HEL and USP data sets), having different numbers of maize hybrids evaluated in different environments for grain yield (GY), plant height (PH), and ear height (EH). Results show that the MDe and the MDs models fitted with the Gaussian kernel (MDe-GK, and MDs-GK) had the highest prediction accuracy. For GY in the HEL data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 9 to 32%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 9 to 49%. For GY in the USP data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 0 to 7%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 34 to 70%. For traits PH and EH, gains in prediction accuracy of models with GK compared to models with GB were smaller than those achieved in GY. Also, these gains in prediction accuracy decreased when a more difficult prediction problem was studied. Copyright © 2017 Bandeira e Sousa et al.

  8. Genotype by environment (climate) interaction improves genomic prediction for production traits in US Holstein cattle.

    PubMed

    Tiezzi, F; de Los Campos, G; Parker Gaddis, K L; Maltecca, C

    2017-03-01

    Genotype by environment interaction (G × E) in dairy cattle productive traits has been shown to exist, but current genetic evaluation methods do not take this component into account. As several environmental descriptors (e.g., climate, farming system) are known to vary within the United States, not accounting for the G × E could lead to reranking of bulls and loss in genetic gain. Using test-day records on milk yield, somatic cell score, fat, and protein percentage from all over the United States, we computed within herd-year-season daughter yield deviations for 1,087 Holstein bulls and regressed them on genetic and environmental information to estimate variance components and to assess prediction accuracy. Genomic information was obtained from a 50k SNP marker panel. Environmental effect inputs included herd (160 levels), geographical region (7 levels), geographical location (2 variables), climate information (7 variables), and management conditions of the herds (16 total variables divided in 4 subgroups). For each set of environmental descriptors, environmental, genomic, and G × E components were sequentially fitted. Variance components estimates confirmed the presence of G × E on milk yield, with its effect being larger than main genetic effect and the environmental effect for some models. Conversely, G × E was moderate for somatic cell score and small for milk composition. Genotype by environment interaction, when included, partially eroded the genomic effect (as compared with the models where G × E was not included), suggesting that the genomic variance could at least in part be attributed to G × E not appropriately accounted for. Model predictive ability was assessed using 3 cross-validation schemes (new bulls, incomplete progeny test, and new environmental conditions), and performance was compared with a reference model including only the main genomic effect. In each scenario, at least 1 of the models including G × E was able to perform better than

  9. Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Willerslev, Eske [University of Copenhagen

    2016-07-12

    Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  10. Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Willerslev, Eske

    2012-03-21

    Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  11. Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study.

    PubMed

    Sikkink, Kristin L; Kobiela, Megan E; Snell-Rood, Emilie C

    2017-05-26

    Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades. First, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population. Taken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and

  12. Regulation of Flowering in Brachypodium distachyon (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Amasino, Rick

    2013-03-01

    Rick Amasino of the University of Wisconsin on "Regulation of Flowering in Brachypodium distachyon" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  13. PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Schadt, Christopher

    2013-03-01

    Christopher Schadt of Oak Ridge National Laboratory on "Plant-Microbe Interactions" in the context of poplar trees at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 held in Walnut Creek, Calif.

  14. Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Saintpaul Strain S-70, Isolated from an Aquatic Environment

    PubMed Central

    Estrada-Acosta, Mitzi; Medrano-Félix, Andrés; Jiménez, Maribel; Gómez-Gil, Bruno; León-Félix, Josefina; Amarillas, Luis

    2013-01-01

    Salmonella is a pathogen of worldwide importance, causing disease in a vast range of hosts, including humans. We report the genome sequence of Salmonella enterica subsp. enterica serotype Saintpaul strain S-70, isolated from an aquatic environment. PMID:24336367

  15. Improving biofuel feedstocks by modifying xylan biosynthesis (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Lau, Jane

    2013-03-01

    Jane Lau of the Joint BioEnergy Institute on "Improving biofuel feedstocks by modifying xylan biosynthesis" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  16. Draft Genome Sequence of Rhodococcus erythropolis NSX2, an Actinobacterium Isolated from a Cadmium-Contaminated Environment

    PubMed Central

    Egidi, Eleonora; Wood, Jennifer L.; Fox, Edward M.; Liu, Wuxing

    2016-01-01

    Rhodococcus erythropolis NSX2 is a rhizobacterium isolated from a heavy metal–contaminated environment. The 6.2-Mb annotated genome sequence shows that this strain harbors genes associated with heavy-metal resistance and xenobiotics degradation. PMID:27795276

  17. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Gallivan, Justin [Emory University

    2016-07-12

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  18. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Gallivan, Justin

    2012-03-21

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  19. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.

    PubMed

    Wisniewski-Dyé, Florence; Borziak, Kirill; Khalsa-Moyers, Gurusahai; Alexandre, Gladys; Sukharnikov, Leonid O; Wuichet, Kristin; Hurst, Gregory B; McDonald, W Hayes; Robertson, Jon S; Barbe, Valérie; Calteau, Alexandra; Rouy, Zoé; Mangenot, Sophie; Prigent-Combaret, Claire; Normand, Philippe; Boyer, Mickaël; Siguier, Patricia; Dessaux, Yves; Elmerich, Claudine; Condemine, Guy; Krishnen, Ganisan; Kennedy, Ivan; Paterson, Andrew H; González, Victor; Mavingui, Patrick; Zhulin, Igor B

    2011-12-01

    Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land.

  20. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

    PubMed Central

    Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

    2011-01-01

    The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies. PMID:20668487

  1. Genome-wide gene-environment interaction analysis for asbestos exposure in lung cancer susceptibility.

    PubMed

    Wei, Sheng; Wang, Li-E; McHugh, Michelle K; Han, Younghun; Xiong, Momiao; Amos, Christopher I; Spitz, Margaret R; Wei, Qingyi Wei

    2012-08-01

    Asbestos exposure is a known risk factor for lung cancer. Although recent genome-wide association studies (GWASs) have identified some novel loci for lung cancer risk, few addressed genome-wide gene-environment interactions. To determine gene-asbestos interactions in lung cancer risk, we conducted genome-wide gene-environment interaction analyses at levels of single nucleotide polymorphisms (SNPs), genes and pathways, using our published Texas lung cancer GWAS dataset. This dataset included 317 498 SNPs from 1154 lung cancer cases and 1137 cancer-free controls. The initial SNP-level P-values for interactions between genetic variants and self-reported asbestos exposure were estimated by unconditional logistic regression models with adjustment for age, sex, smoking status and pack-years. The P-value for the most significant SNP rs13383928 was 2.17×10(-6), which did not reach the genome-wide statistical significance. Using a versatile gene-based test approach, we found that the top significant gene was C7orf54, located on 7q32.1 (P = 8.90×10(-5)). Interestingly, most of the other significant genes were located on 11q13. When we used an improved gene-set-enrichment analysis approach, we found that the Fas signaling pathway and the antigen processing and presentation pathway were most significant (nominal P < 0.001; false discovery rate < 0.05) among 250 pathways containing 17 572 genes. We believe that our analysis is a pilot study that first describes the gene-asbestos interaction in lung cancer risk at levels of SNPs, genes and pathways. Our findings suggest that immune function regulation-related pathways may be mechanistically involved in asbestos-associated lung cancer risk.

  2. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.

    PubMed

    Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

    2011-02-01

    The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies.

  3. A Genomic Bayesian Multi-trait and Multi-environment Model

    PubMed Central

    Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H.; Pérez-Hernández, Oscar; Eskridge, Kent M.; Rutkoski, Jessica

    2016-01-01

    When information on multiple genotypes evaluated in multiple environments is recorded, a multi-environment single trait model for assessing genotype × environment interaction (G × E) is usually employed. Comprehensive models that simultaneously take into account the correlated traits and trait × genotype × environment interaction (T × G × E) are lacking. In this research, we propose a Bayesian model for analyzing multiple traits and multiple environments for whole-genome prediction (WGP) model. For this model, we used Half-t priors on each standard deviation term and uniform priors on each correlation of the covariance matrix. These priors were not informative and led to posterior inferences that were insensitive to the choice of hyper-parameters. We also developed a computationally efficient Markov Chain Monte Carlo (MCMC) under the above priors, which allowed us to obtain all required full conditional distributions of the parameters leading to an exact Gibbs sampling for the posterior distribution. We used two real data sets to implement and evaluate the proposed Bayesian method and found that when the correlation between traits was high (>0.5), the proposed model (with unstructured variance–covariance) improved prediction accuracy compared to the model with diagonal and standard variance–covariance structures. The R-software package Bayesian Multi-Trait and Multi-Environment (BMTME) offers optimized C++ routines to efficiently perform the analyses. PMID:27342738

  4. A Genomic Bayesian Multi-trait and Multi-environment Model.

    PubMed

    Montesinos-López, Osval A; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H; Pérez-Hernández, Oscar; Eskridge, Kent M; Rutkoski, Jessica

    2016-09-08

    When information on multiple genotypes evaluated in multiple environments is recorded, a multi-environment single trait model for assessing genotype × environment interaction (G × E) is usually employed. Comprehensive models that simultaneously take into account the correlated traits and trait × genotype × environment interaction (T × G × E) are lacking. In this research, we propose a Bayesian model for analyzing multiple traits and multiple environments for whole-genome prediction (WGP) model. For this model, we used Half-[Formula: see text] priors on each standard deviation term and uniform priors on each correlation of the covariance matrix. These priors were not informative and led to posterior inferences that were insensitive to the choice of hyper-parameters. We also developed a computationally efficient Markov Chain Monte Carlo (MCMC) under the above priors, which allowed us to obtain all required full conditional distributions of the parameters leading to an exact Gibbs sampling for the posterior distribution. We used two real data sets to implement and evaluate the proposed Bayesian method and found that when the correlation between traits was high (>0.5), the proposed model (with unstructured variance-covariance) improved prediction accuracy compared to the model with diagonal and standard variance-covariance structures. The R-software package Bayesian Multi-Trait and Multi-Environment (BMTME) offers optimized C++ routines to efficiently perform the analyses. Copyright © 2016 Montesinos-López et al.

  5. The First Pilot Genome-Wide Gene-Environment Study of Depression in the Japanese Population

    PubMed Central

    Otowa, Takeshi; Kawamura, Yoshiya; Tsutsumi, Akizumi; Kawakami, Norito; Kan, Chiemi; Shimada, Takafumi; Umekage, Tadashi; Kasai, Kiyoto; Tokunaga, Katsushi; Sasaki, Tsukasa

    2016-01-01

    Stressful events have been identified as a risk factor for depression. Although gene–environment (G × E) interaction in a limited number of candidate genes has been explored, no genome-wide search has been reported. The aim of the present study is to identify genes that influence the association of stressful events with depression. Therefore, we performed a genome-wide G × E interaction analysis in the Japanese population. A genome-wide screen with 320 subjects was performed using the Affymetrix Genome-Wide Human Array 6.0. Stressful life events were assessed using the Social Readjustment Rating Scale (SRRS) and depression symptoms were assessed with self-rating questionnaires using the Center for Epidemiologic Studies Depression (CES-D) scale. The p values for interactions between single nucleotide polymorphisms (SNPs) and stressful events were calculated using the linear regression model adjusted for sex and age. After quality control of genotype data, a total of 534,848 SNPs on autosomal chromosomes were further analyzed. Although none surpassed the level of the genome-wide significance, a marginal significant association of interaction between SRRS and rs10510057 with depression were found (p = 4.5 × 10−8). The SNP is located on 10q26 near Regulators of G-protein signaling 10 (RGS10), which encodes a regulatory molecule involved in stress response. When we investigated a similar G × E interaction between depression (K6 scale) and work-related stress in an independent sample (n = 439), a significant G × E effect on depression was observed (p = 0.015). Our findings suggest that rs10510057, interacting with stressors, may be involved in depression risk. Incorporating G × E interaction into GWAS can contribute to find susceptibility locus that are potentially missed by conventional GWAS. PMID:27529621

  6. Evolutionary dynamics of an at-rich satellite DNA and its contribution to karyotype differentiation in wild diploid Arachis species.

    PubMed

    Samoluk, Sergio Sebastián; Robledo, Germán; Bertioli, David; Seijo, José Guillermo

    2017-04-01

    Satellite DNA (satDNA) is a major component of the heterochromatic regions of eukaryote genomes and usually shows a high evolutionary dynamic, even among closely related species. Section Arachis (genus Arachis) is composed of species belonging to six different genomes (A, B, D, F, G and K). The most distinguishing features among these genomes are the amount and distribution of the heterochromatin in the karyotypes. With the objective of gaining insight into the sequence composition and evolutionary dynamics of the heterochromatin fraction in Arachis, we investigated here the sequence diversity, genomic abundance, and chromosomal distribution of a satDNA family (ATR-2) among seven diploid species of section Arachis. All of the isolated sequences were AT-rich and highly conserved at both intraspecific and interspecific levels, without any species-specific polymorphism. Pairwise comparisons of isolated ATR-2 monomers revealed that most of the nucleotide sites were in the first two transitional stages of Strachan's model. However, the abundance of ATR-2 was significantly different among genomes according to the 'library hypothesis'. Fluorescent in situ hybridization revealed that ATR-2 is a main component of the DAPI(+) centromeric heterochromatin of the A, F, and K genomes. Thus, the evolution of the different heterochromatin patterns observed in Arachis genomes can be explained, at least in part, by the differential representation of ATR-2 among the different species or even among the chromosomes of the same complement. These findings are the first to demonstrate the participation of satDNA sequences in the karyotype diversification of wild diploid Arachis species.

  7. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

    PubMed

    Rouxel, Thierry; Grandaubert, Jonathan; Hane, James K; Hoede, Claire; van de Wouw, Angela P; Couloux, Arnaud; Dominguez, Victoria; Anthouard, Véronique; Bally, Pascal; Bourras, Salim; Cozijnsen, Anton J; Ciuffetti, Lynda M; Degrave, Alexandre; Dilmaghani, Azita; Duret, Laurent; Fudal, Isabelle; Goodwin, Stephen B; Gout, Lilian; Glaser, Nicolas; Linglin, Juliette; Kema, Gert H J; Lapalu, Nicolas; Lawrence, Christopher B; May, Kim; Meyer, Michel; Ollivier, Bénédicte; Poulain, Julie; Schoch, Conrad L; Simon, Adeline; Spatafora, Joseph W; Stachowiak, Anna; Turgeon, B Gillian; Tyler, Brett M; Vincent, Delphine; Weissenbach, Jean; Amselem, Joëlle; Quesneville, Hadi; Oliver, Richard P; Wincker, Patrick; Balesdent, Marie-Hélène; Howlett, Barbara J

    2011-02-15

    Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.

  8. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes.

    PubMed

    Sun, Jin; Zhang, Yu; Xu, Ting; Zhang, Yang; Mu, Huawei; Zhang, Yanjie; Lan, Yi; Fields, Christopher J; Hui, Jerome Ho Lam; Zhang, Weipeng; Li, Runsheng; Nong, Wenyan; Cheung, Fiona Ka Man; Qiu, Jian-Wen; Qian, Pei-Yuan

    2017-04-03

    Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.

  9. Genomics of Secondary Metabolism in Populus: Interactions with Biotic and Abiotic Environments

    SciTech Connect

    Chen, F.; Liu, C.; Tschaplinski, T. J.; Zhao, N.

    2009-09-01

    Populus trees face constant challenges from the environment during their life cycle. To ensure their survival and reproduction, Populus trees deploy various types of defenses, one of which is the production of a myriad of secondary metabolites. Compounds derived from the shikimate-phenylpropanoid pathway are the most abundant class of secondary metabolites synthesized in Populus. Among other major classes of secondary metabolites in Populus are terpenoids and fatty acid-derivatives. Some of the secondary metabolites made by Populus trees have been functionally characterized. Some others have been associated with certain biological/ecological processes, such as defense against insects and microbial pathogens or acclimation or adaptation to abiotic stresses. Functions of many Populus secondary metabolites remain unclear. The advent of various novel genomic tools will enable us to explore in greater detail the complexity of secondary metabolism in Populus. Detailed data mining of the Populus genome sequence can unveil candidate genes of secondary metabolism. Metabolomic analysis will continue to identify new metabolites synthesized in Populus. Integrated genomics that combines various 'omics' tools will prove to be the most powerful approach in revealing the molecular and biochemical basis underlying the biosynthesis of secondary metabolites in Populus. Characterization of the biological/ecological functions of secondary metabolites as well as their biosynthesis will provide knowledge and tools for genetically engineering the production of seconday metabolites that can lead to the generation of novel, improved Populus varieties.

  10. Phenotypic Plasticity Promotes Balanced Polymorphism in Periodic Environments by a Genomic Storage Effect

    PubMed Central

    Gulisija, Davorka; Kim, Yuseob; Plotkin, Joshua B.

    2016-01-01

    Phenotypic plasticity is known to evolve in perturbed habitats, where it alleviates the deleterious effects of selection. But the effects of plasticity on levels of genetic polymorphism, an important precursor to adaptation in temporally varying environments, are unclear. Here we develop a haploid, two-locus population-genetic model to describe the interplay between a plasticity modifier locus and a target locus subject to periodically varying selection. We find that the interplay between these two loci can produce a “genomic storage effect” that promotes balanced polymorphism over a large range of parameters, in the absence of all other conditions known to maintain genetic variation. The genomic storage effect arises as recombination allows alleles at the two loci to escape more harmful genetic backgrounds and associate in haplotypes that persist until environmental conditions change. Using both Monte Carlo simulations and analytical approximations we quantify the strength of the genomic storage effect across a range of selection pressures, recombination rates, plasticity modifier effect sizes, and environmental periods. PMID:26857626

  11. Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants.

    PubMed

    Karpinets, Tatiana V; Park, Byung H; Syed, Mustafa H; Klotz, Martin G; Uberbacher, Edward C

    2014-07-01

    Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study comparatively analyzed the genomes of 54 mutualists and pathogens to discover genomic markers associated with the different phenotypes. Using metabolic network models, we predict external environments associated with free-living and symbiotic lifestyles and quantify dependences of symbionts on the host in terms of the consumed metabolites. We show that specific differences between the phenotypes are pronounced at the levels of metabolic enzymes, especially carbohydrate active, and protein functions. Overall, biosynthetic functions are enriched and more diverse in plant mutualists whereas processes and functions involved in degradation and host invasion are enriched and more diverse in pathogens. A distinctive characteristic of plant pathogens is a putative novel secretion system with a circadian rhythm regulator. A specific marker of plant mutualists is the co-residence of genes encoding nitrogenase and ribulose bisphosphate carboxylase/oxygenase (RuBisCO). We predict that RuBisCO is likely used in a putative metabolic pathway to supplement carbon obtained heterotrophically with low-cost assimilation of carbon from CO2. We validate results of the comparative analysis by predicting correct phenotype, pathogenic or mutualistic, for 20 symbionts in an independent set of 30 pathogens, mutualists, and commensals.

  12. Phenotypic Plasticity Promotes Balanced Polymorphism in Periodic Environments by a Genomic Storage Effect.

    PubMed

    Gulisija, Davorka; Kim, Yuseob; Plotkin, Joshua B

    2016-04-01

    Phenotypic plasticity is known to evolve in perturbed habitats, where it alleviates the deleterious effects of selection. But the effects of plasticity on levels of genetic polymorphism, an important precursor to adaptation in temporally varying environments, are unclear. Here we develop a haploid, two-locus population-genetic model to describe the interplay between a plasticity modifier locus and a target locus subject to periodically varying selection. We find that the interplay between these two loci can produce a "genomic storage effect" that promotes balanced polymorphism over a large range of parameters, in the absence of all other conditions known to maintain genetic variation. The genomic storage effect arises as recombination allows alleles at the two loci to escape more harmful genetic backgrounds and associate in haplotypes that persist until environmental conditions change. Using both Monte Carlo simulations and analytical approximations we quantify the strength of the genomic storage effect across a range of selection pressures, recombination rates, plasticity modifier effect sizes, and environmental periods.

  13. Genomic imprinting effects in a compromised in utero environment: implications for a healthy pregnancy.

    PubMed

    Lim, A L; Ferguson-Smith, A C

    2010-04-01

    Genomic imprinting in gametogenesis marks a subset of mammalian genes for parent-of-origin-dependent monoallelic expression in the offspring. In mice, the identification and manipulation of individual imprinted genes has shown that the diverse products of these genes are largely devoted to controlling pre- and postnatal growth. Human syndromes with parental origin effects have been characterized both at the phenotypic and genotypic levels, allowing further elucidation of the function and regulation of imprinted genes. Evidence suggests that a compromised in utero environment influences fetal growth through the modulation of epigenetic states. However it is not known whether imprinted genes, by their nature, might be more or less susceptible to such environmental influences. Here we review the progress made in addressing the influence of a compromised in utero environment on the behavior of imprinted genes. We also examine whether these environmental influences may have an impact on the later development of human disease.

  14. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions

    PubMed Central

    Bellas, Christopher M.; Anesio, Alexandre M.; Barker, Gary

    2015-01-01

    Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts

  15. The Genome of Spironucleus salmonicida Highlights a Fish Pathogen Adapted to Fluctuating Environments

    PubMed Central

    Xu, Feifei; Jerlström-Hultqvist, Jon; Einarsson, Elin; Ástvaldsson, Ásgeir; Svärd, Staffan G.; Andersson, Jan O.

    2014-01-01

    Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host. PMID:24516394

  16. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions.

    PubMed

    Bellas, Christopher M; Anesio, Alexandre M; Barker, Gary

    2015-01-01

    Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts.

  17. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

    USDA-ARS?s Scientific Manuscript database

    Genotype by environment interaction (G*E) is one of the key issues when analyzing phenotypes. The use of environment data to model G*E has long been a subject of interest but is limited by the same problems as those addressed by genomic selection GS methods: a large number of correlated predictors e...

  18. Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment.

    PubMed

    Xu, Jian; Li, Jiong-Tang; Jiang, Yanliang; Peng, Wenzhu; Yao, Zongli; Chen, Baohua; Jiang, Likun; Feng, Jingyan; Ji, Peifeng; Liu, Guiming; Liu, Zhanjiang; Tai, Ruyu; Dong, Chuanju; Sun, Xiaoqing; Zhao, Zi-Xia; Zhang, Yan; Wang, Jian; Li, Shangqi; Zhao, Yunfeng; Yang, Jiuhui; Sun, Xiaowen; Xu, Peng

    2017-01-01

    The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L (pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding egg coat proteins and natriuretic peptide receptors, possibly underlying the adaptation to extreme environmental stress. We further sequenced the genomes of 10 additional individuals from freshwater and 18 from Lake Dali Nur populations, and we detected a total of 7.6 million SNPs from both populations. In a genome scan and comparison of these two populations, we identified a set of genomic regions under selective sweeps that harbor genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion. Our findings provide comprehensive insight into the genomic mechanisms of teleost fish that underlie their adaptation to extreme alkaline environments. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments.

    PubMed

    Taş, Neslihan; van Eekert, Miriam H A; de Vos, Willem M; Smidt, Hauke

    2010-07-01

    The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely 'Dehalococcoides' spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase-encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments. © 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

  20. Applications of the pipeline environment for visual informatics and genomics computations.

    PubMed

    Dinov, Ivo D; Torri, Federica; Macciardi, Fabio; Petrosyan, Petros; Liu, Zhizhong; Zamanyan, Alen; Eggert, Paul; Pierce, Jonathan; Genco, Alex; Knowles, James A; Clark, Andrew P; Van Horn, John D; Ames, Joseph; Kesselman, Carl; Toga, Arthur W

    2011-07-26

    Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power

  1. Applications of the pipeline environment for visual informatics and genomics computations

    PubMed Central

    2011-01-01

    Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client

  2. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters

    PubMed Central

    Lavender, Christopher A.; Hoffman, Jackson A.; Trotter, Kevin W.; Gilchrist, Daniel A.; Bennett, Brian D.; Burkholder, Adam B.; Fargo, David C.; Archer, Trevor K.

    2016-01-01

    Antisense transcription is a prevalent feature at mammalian promoters. Previous studies have primarily focused on antisense transcription initiating upstream of genes. Here, we characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human breast cancer cells, investigating the genomic context of downstream antisense transcription. We find extensive correlations between antisense transcription and features associated with the chromatin environment at gene promoters. Antisense transcription downstream of promoters is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites. Antisense transcription initiates between nucleosomes regularly positioned downstream of these promoters. The nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac. This region is bound by chromatin remodeling and histone modifying complexes including SWI/SNF subunits and HDACs, suggesting that antisense transcription or resulting RNA transcripts contribute to the creation and maintenance of a promoter-associated chromatin environment. Downstream antisense transcription overlays additional regulatory features, such as transcription factor binding, DNA accessibility, and the downstream edge of promoter-associated CpG islands. These features suggest an important role for antisense transcription in the regulation of gene expression and the maintenance of a promoter-associated chromatin environment. PMID:27487356

  3. Meta-regression of gene-environment interaction in genome-wide association studies.

    PubMed

    Xu, Xiaoxiao; Shi, Gang; Nehorai, Arye

    2013-12-01

    Genome-wide association studies (GWAS) have created heightened interest in understanding the effects of gene-environment interaction on complex human diseases or traits. Applying methods for analyzing such interaction can help uncover novel genes and identify environmental hazards that influence only certain genetically susceptible groups. However, the number of interaction analysis methods is still limited, so there is a need to develop more efficient and powerful methods. In this paper, we propose two novel meta-analysis methods of studying gene-environment interaction, based on meta-regression of estimated genetic effects on the environmental factor. The two methods can perform joint analysis of a single nucleotide polymorphism's (SNP) main and interaction effects, or analyze only the effect of the interaction. They can readily estimate any linear or non-linear interactions by simply modifying the gene-environment regression function. Thus, they are efficient methods to be applied to different scenarios. We use numerical examples to demonstrate the performance of our methods. We also compare them with two other methods commonly used in current GWAS, i.e., meta-analysis of SNP main effects (MAIN) and joint meta-analysis of SNP main and interaction effects (JMA). The results show that our methods are more powerful than MAIN when the interaction effect exists, and are comparable to JMAin the linear or quadratic interaction cases. In the numerical examples, we also investigate how the number of the divided groups and the sample size of the studies affect the performance of our methods.

  4. Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.

    PubMed

    Takagi, Haruna; Inai, Yuta; Watanabe, Shun-ichiro; Tatemoto, Sayuri; Yajima, Mamiko; Akasaka, Koji; Yamamoto, Takashi; Sakamoto, Naoaki

    2012-01-01

    The Ars insulator is a boundary element identified in the upstream region of the arylsulfatase (HpArs) gene in the sea urchin, Hemicentrotus pulcherrimus, and possesses the ability to both block enhancer-promoter communications and protect transgenes from silent chromatin. To understand the molecular mechanism of the Ars insulator, we investigated the correlation between chromatin structure, DNA structure and insulator activity. Nuclease digestion of nuclei isolated from sea urchin embryos revealed the presence of a nuclease-hypersensitive site within the Ars insulator. Analysis of micrococcal nuclease-sensitive sites in the Ars insulator, reconstituted with nucleosomes, showed the exclusion of nucleosomes from the central AT-rich region. Furthermore, the central AT-rich region in naked DNA was sensitive to nucleotide base modification by diethylpyrocarbonate (DEPC). These observations suggest that non-B-DNA structures in the central AT-rich region may inhibit nucleosomal formation, which leads to nuclease hypersensitivity. Furthermore, comparison of nucleotide sequences between the HpArs gene and its ortholog in Strongylocentrotus purpuratus revealed that the central AT-rich region of the Ars insulator is conserved, and this conserved region showed significant enhancer blocking activity. These results suggest that the central AT-rich nucleosome-free region plays an important role in the function of the Ars insulator.

  5. Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

    PubMed

    Maeso, Ignacio; Tena, Juan J

    2016-09-01

    Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

    PubMed Central

    Khalsa-Moyers, Gurusahai; Alexandre, Gladys; Sukharnikov, Leonid O.; Wuichet, Kristin; Hurst, Gregory B.; McDonald, W. Hayes; Robertson, Jon S.; Barbe, Valérie; Calteau, Alexandra; Rouy, Zoé; Mangenot, Sophie; Prigent-Combaret, Claire; Normand, Philippe; Boyer, Mickaël; Siguier, Patricia; Dessaux, Yves; Elmerich, Claudine; Condemine, Guy; Krishnen, Ganisan; Kennedy, Ivan; Paterson, Andrew H.; González, Victor; Mavingui, Patrick; Zhulin, Igor B.

    2011-01-01

    Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that “hydrobacteria” and “terrabacteria” might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land. PMID:22216014

  7. Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

    PubMed Central

    Campbell, Barbara J.; Smith, Julie L.; Hanson, Thomas E.; Klotz, Martin G.; Stein, Lisa Y.; Lee, Charles K.; Wu, Dongying; Robinson, Jeffrey M.; Khouri, Hoda M.; Eisen, Jonathan A.; Cary, S. Craig

    2009-01-01

    Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment—some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20°C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere—anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles

  8. Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments

    PubMed Central

    McRose, Darcy L.; Zhang, Xinning; Kraepiel, Anne M. L.; Morel, François M. M.

    2017-01-01

    The nitrogenase enzyme, which catalyzes the reduction of N2 gas to NH4+, occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient ‘canonical’ Mo-nitrogenase, whereas Fe-only and V-(‘alternative’) nitrogenases are often considered ‘backup’ enzymes, used when Mo is limiting. Yet, the environmental distribution and diversity of alternative nitrogenases remains largely unknown. We searched for alternative nitrogenase genes in sequenced genomes and used PacBio sequencing to explore the diversity of canonical (nifD) and alternative (anfD and vnfD) nitrogenase amplicons in two coastal environments: the Florida Everglades and Sippewissett Marsh (MA). Genome-based searches identified an additional 25 species and 10 genera not previously known to encode alternative nitrogenases. Alternative nitrogenase amplicons were found in both Sippewissett Marsh and the Florida Everglades and their activity was further confirmed using newly developed isotopic techniques. Conserved amino acid sequences corresponding to cofactor ligands were also analyzed in anfD and vnfD amplicons, offering insight into environmental variants of these motifs. This study increases the number of available anfD and vnfD sequences ∼20-fold and allows for the first comparisons of environmental Mo-, Fe-only, and V-nitrogenase diversity. Our results suggest that alternative nitrogenases are maintained across a range of organisms and environments and that they can make important contributions to nitrogenase diversity and nitrogen fixation. PMID:28293220

  9. Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment

    PubMed Central

    2013-01-01

    Background Streptococcus agalactiae is a major cause of bovine mastitis, which is the dominant health disorder affecting milk production within the dairy industry and is responsible for substantial financial losses to the industry worldwide. However, there is considerable evidence for host adaptation (ecotypes) within S. agalactiae, with both bovine and human sourced isolates showing a high degree of distinctiveness, suggesting differing ability to cause mastitis. Here, we (i) generate RNAseq data from three S. agalactiae isolates (two putative bovine adapted and one human) and (ii) compare publicly available whole genome shotgun sequence data from an additional 202 isolates, obtained from six host species, to elucidate possible genetic factors/adaptations likely important for S. agalactiae growth and survival in the bovine mammary gland. Results Tests for differential expression showed distinct expression profiles for the three isolates when grown in bovine milk. A key finding for the two putatively bovine adapted isolates was the up regulation of a lactose metabolism operon (Lac.2) that was strongly correlated with the bovine environment (all 36 bovine sourced isolates on GenBank possessed the operon, in contrast to only 8/151 human sourced isolates). Multi locus sequence typing of all genome sequences and phylogenetic analysis using conserved operon genes from 44 S. agalactiae isolates and 16 additional Streptococcus species provided strong evidence for acquisition of the operon via multiple lateral gene transfer events, with all Streptococcus species known to be major causes of mastitis, identified as possible donors. Furthermore, lactose fermentation tests were only positive for isolates possessing Lac.2. Combined, these findings suggest that lactose metabolism is likely an important adaptation to the bovine environment. Additional up regulation in the bovine adapted isolates included genes involved in copper homeostasis, metabolism of purine, pyrimidine

  10. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

    PubMed Central

    Kim, E-S; Elbeltagy, A R; Aboul-Naga, A M; Rischkowsky, B; Sayre, B; Mwacharo, J M; Rothschild, M F

    2016-01-01

    Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping. PMID:26555032

  11. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

    PubMed

    Kim, E-S; Elbeltagy, A R; Aboul-Naga, A M; Rischkowsky, B; Sayre, B; Mwacharo, J M; Rothschild, M F

    2016-03-01

    Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

  12. Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents

    PubMed Central

    2009-01-01

    Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs), which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution. PMID:20038498

  13. Needles: Toward Large-Scale Genomic Prediction with Marker-by-Environment Interaction.

    PubMed

    De Coninck, Arne; De Baets, Bernard; Kourounis, Drosos; Verbosio, Fabio; Schenk, Olaf; Maenhout, Steven; Fostier, Jan

    2016-05-01

    Genomic prediction relies on genotypic marker information to predict the agronomic performance of future hybrid breeds based on trial records. Because the effect of markers may vary substantially under the influence of different environmental conditions, marker-by-environment interaction effects have to be taken into account. However, this may lead to a dramatic increase in the computational resources needed for analyzing large-scale trial data. A high-performance computing solution, called Needles, is presented for handling such data sets. Needles is tailored to the particular properties of the underlying algebraic framework by exploiting a sparse matrix formalism where suited and by utilizing distributed computing techniques to enable the use of a dedicated computing cluster. It is demonstrated that large-scale analyses can be performed within reasonable time frames with this framework. Moreover, by analyzing simulated trial data, it is shown that the effects of markers with a high environmental interaction can be predicted more accurately when more records per environment are available in the training data. The availability of such data and their analysis with Needles also may lead to the discovery of highly contributing QTL in specific environmental conditions. Such a framework thus opens the path for plant breeders to select crops based on these QTL, resulting in hybrid lines with optimized agronomic performance in specific environmental conditions.

  14. Genome-wide gene-environment interactions on quantitative traits using family data.

    PubMed

    Sitlani, Colleen M; Dupuis, Josée; Rice, Kenneth M; Sun, Fangui; Pitsillides, Achilleas N; Cupples, L Adrienne; Psaty, Bruce M

    2016-07-01

    Gene-environment interactions may provide a mechanism for targeting interventions to those individuals who would gain the most benefit from them. Searching for interactions agnostically on a genome-wide scale requires large sample sizes, often achieved through collaboration among multiple studies in a consortium. Family studies can contribute to consortia, but to do so they must account for correlation within families by using specialized analytic methods. In this paper, we investigate the performance of methods that account for within-family correlation, in the context of gene-environment interactions with binary exposures and quantitative outcomes. We simulate both cross-sectional and longitudinal measurements, and analyze the simulated data taking family structure into account, via generalized estimating equations (GEE) and linear mixed-effects models. With sufficient exposure prevalence and correct model specification, all methods perform well. However, when models are misspecified, mixed modeling approaches have seriously inflated type I error rates. GEE methods with robust variance estimates are less sensitive to model misspecification; however, when exposures are infrequent, GEE methods require modifications to preserve type I error rate. We illustrate the practical use of these methods by evaluating gene-drug interactions on fasting glucose levels in data from the Framingham Heart Study, a cohort that includes related individuals.

  15. Unifying Genetic Canalization, Genetic Constraint, and Genotype-by-Environment Interaction: QTL by Genomic Background by Environment Interaction of Flowering Time in Boechera stricta

    PubMed Central

    Lee, Cheng-Ruei; Anderson, Jill T.; Mitchell-Olds, Thomas

    2014-01-01

    Natural populations exhibit substantial variation in quantitative traits. A quantitative trait is typically defined by its mean and variance, and to date most genetic mapping studies focus on loci altering trait means but not (co)variances. For single traits, the control of trait variance across genetic backgrounds is referred to as genetic canalization. With multiple traits, the genetic covariance among different traits in the same environment indicates the magnitude of potential genetic constraint, while genotype-by-environment interaction (GxE) concerns the same trait across different environments. While some have suggested that these three attributes of quantitative traits are different views of similar concepts, it is not yet clear, however, whether they have the same underlying genetic mechanism. Here, we detect quantitative trait loci (QTL) influencing the (co)variance of phenological traits in six distinct environments in Boechera stricta, a close relative of Arabidopsis. We identified nFT as the QTL altering the magnitude of phenological trait canalization, genetic constraint, and GxE. Both the magnitude and direction of nFT's canalization effects depend on the environment, and to our knowledge, this reversibility of canalization across environments has not been reported previously. nFT's effects on trait covariance structure (genetic constraint and GxE) likely result from the variable and reversible canalization effects across different traits and environments, which can be explained by the interaction among nFT, genomic backgrounds, and environmental stimuli. This view is supported by experiments demonstrating significant nFT by genomic background epistatic interactions affecting phenological traits and expression of the candidate gene, FT. In contrast to the well-known canalization gene Hsp90, the case of nFT may exemplify an alternative mechanism: Our results suggest that (at least in traits with major signal integrators such as flowering time) genetic

  16. The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment

    PubMed Central

    Alcaraz, Luis David; Olmedo, Gabriela; Bonilla, Germán; Cerritos, René; Hernández, Gustavo; Cruz, Alfredo; Ramírez, Enrique; Putonti, Catherine; Jiménez, Beatriz; Martínez, Eva; López, Varinia; Arvizu, Jacqueline L.; Ayala, Francisco; Razo, Francisco; Caballero, Juan; Siefert, Janet; Eguiarte, Luis; Vielle, Jean-Philippe; Martínez, Octavio; Souza, Valeria; Herrera-Estrella, Alfredo; Herrera-Estrella, Luis

    2008-01-01

    The Cuatro Ciénegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system poor in NaCl, rich in sulfates, and with extremely low phosphorus levels (<0.3 μM). Here, we report the complete genome sequence of Bacillus coahuilensis, a sporulating bacterium isolated from the water column of a desiccation lagoon in CCB. At 3.35 Megabases this is the smallest genome sequenced to date of a Bacillus species and provides insights into the origin, evolution, and adaptation of B. coahuilensis to the CCB environment. We propose that the size and complexity of the B. coahuilensis genome reflects the adaptation of an ancient marine bacterium to a novel environment, providing support to a “marine isolation origin hypothesis” that is consistent with the geology of CCB. This genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high-light environments. The B. coahuilensis genome sequence also revealed important ecological features of the bacterial community in CCB and offers opportunities for a unique glimpse of a microbe-dominated world last seen in the Precambrian. PMID:18408155

  17. The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.

    PubMed

    Alcaraz, Luis David; Olmedo, Gabriela; Bonilla, Germán; Cerritos, René; Hernández, Gustavo; Cruz, Alfredo; Ramírez, Enrique; Putonti, Catherine; Jiménez, Beatriz; Martínez, Eva; López, Varinia; Arvizu, Jacqueline L; Ayala, Francisco; Razo, Francisco; Caballero, Juan; Siefert, Janet; Eguiarte, Luis; Vielle, Jean-Philippe; Martínez, Octavio; Souza, Valeria; Herrera-Estrella, Alfredo; Herrera-Estrella, Luis

    2008-04-15

    The Cuatro Ciénegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system poor in NaCl, rich in sulfates, and with extremely low phosphorus levels (<0.3 microM). Here, we report the complete genome sequence of Bacillus coahuilensis, a sporulating bacterium isolated from the water column of a desiccation lagoon in CCB. At 3.35 Megabases this is the smallest genome sequenced to date of a Bacillus species and provides insights into the origin, evolution, and adaptation of B. coahuilensis to the CCB environment. We propose that the size and complexity of the B. coahuilensis genome reflects the adaptation of an ancient marine bacterium to a novel environment, providing support to a "marine isolation origin hypothesis" that is consistent with the geology of CCB. This genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high-light environments. The B. coahuilensis genome sequence also revealed important ecological features of the bacterial community in CCB and offers opportunities for a unique glimpse of a microbe-dominated world last seen in the Precambrian.

  18. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Sayre, Richard [LANL

    2016-07-12

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  19. Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Oranienburg Strain S-76, Isolated from an Aquatic Environment

    PubMed Central

    Medrano-Félix, Andrés; Estrada-Acosta, Mitzi; Jiménez, Maribel; Gómez-Gil, Bruno; León-Félix, Josefina; Amarillas, Luis

    2013-01-01

    Salmonella is a widespread microorganism and a common causative agent of food-borne illnesses. Salmonella enterica subsp. enterica serotype Oranienburg is highly prevalent in surface water from tropical ecosystems and is not commonly related to illnesses. Here, we report the first genome sequence of Salmonella Oranienburg strain S-76, isolated from an aquatic environment. PMID:24336368

  20. Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Brady, Siobhan [UC Davis

    2016-07-12

    Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  1. Draft Genome Sequence of Rhodococcus erythropolis NSX2, an Actinobacterium Isolated from a Cadmium-Contaminated Environment.

    PubMed

    Egidi, Eleonora; Wood, Jennifer L; Fox, Edward M; Liu, Wuxing; Franks, Ashley E

    2016-10-20

    Rhodococcus erythropolis NSX2 is a rhizobacterium isolated from a heavy metal-contaminated environment. The 6.2-Mb annotated genome sequence shows that this strain harbors genes associated with heavy-metal resistance and xenobiotics degradation. Copyright © 2016 Egidi et al.

  2. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Sayre, Richard

    2012-03-22

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  3. Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Brady, Siobhan

    2012-03-22

    Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  4. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions.

    PubMed

    Heslot, Nicolas; Akdemir, Deniz; Sorrells, Mark E; Jannink, Jean-Luc

    2014-02-01

    Development of models to predict genotype by environment interactions, in unobserved environments, using environmental covariates, a crop model and genomic selection. Application to a large winter wheat dataset. Genotype by environment interaction (G*E) is one of the key issues when analyzing phenotypes. The use of environment data to model G*E has long been a subject of interest but is limited by the same problems as those addressed by genomic selection methods: a large number of correlated predictors each explaining a small amount of the total variance. In addition, non-linear responses of genotypes to stresses are expected to further complicate the analysis. Using a crop model to derive stress covariates from daily weather data for predicted crop development stages, we propose an extension of the factorial regression model to genomic selection. This model is further extended to the marker level, enabling the modeling of quantitative trait loci (QTL) by environment interaction (Q*E), on a genome-wide scale. A newly developed ensemble method, soft rule fit, was used to improve this model and capture non-linear responses of QTL to stresses. The method is tested using a large winter wheat dataset, representative of the type of data available in a large-scale commercial breeding program. Accuracy in predicting genotype performance in unobserved environments for which weather data were available increased by 11.1% on average and the variability in prediction accuracy decreased by 10.8%. By leveraging agronomic knowledge and the large historical datasets generated by breeding programs, this new model provides insight into the genetic architecture of genotype by environment interactions and could predict genotype performance based on past and future weather scenarios.

  5. Community Genomic Analysis of Strain Variation of a Novel Archaeon in an Acid Mine Drainage Environment

    NASA Astrophysics Data System (ADS)

    Yelton, P.; Banfield, J.; Wilmes, P.

    2006-12-01

    Microorganisms play a significant role in acid mine drainage (AMD) generation within the Richmond Mine, Iron Mountain, California. To better understand the contributions of individual microbial species to this process, the assemblies of community genomic data from AMD biofilms were manually curated. Not reported previously is detailed analysis of genomic sequence from G-plasma, an archaeal population from a sample collected from the 5-way location in 2002. The G-plasma population exhibits a small number of differing nucleotide sequences at most genomic locations and comprises multiple genome types. Linkage between these sequence types indicates frequent homologous recombination. As the near complete genome is still in many fragments, the current investigation focused on the 25% of the genome in large, confidently linked pieces. Many predicted proteins from this organism were detected via proteomic analysis. In combination, information about genome heterogeneity and protein expression is providing clues to the role of this population in the biofilm community.

  6. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

    PubMed

    Li, Cai; Zhang, Yong; Li, Jianwen; Kong, Lesheng; Hu, Haofu; Pan, Hailin; Xu, Luohao; Deng, Yuan; Li, Qiye; Jin, Lijun; Yu, Hao; Chen, Yan; Liu, Binghang; Yang, Linfeng; Liu, Shiping; Zhang, Yan; Lang, Yongshan; Xia, Jinquan; He, Weiming; Shi, Qiong; Subramanian, Sankar; Millar, Craig D; Meader, Stephen; Rands, Chris M; Fujita, Matthew K; Greenwold, Matthew J; Castoe, Todd A; Pollock, David D; Gu, Wanjun; Nam, Kiwoong; Ellegren, Hans; Ho, Simon Yw; Burt, David W; Ponting, Chris P; Jarvis, Erich D; Gilbert, M Thomas P; Yang, Huanming; Wang, Jian; Lambert, David M; Wang, Jun; Zhang, Guojie

    2014-01-01

    Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.

  7. Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection.

    PubMed

    Anderson, Jill T; Lee, Cheng-Ruei; Mitchell-Olds, Thomas

    2014-01-01

    Fitness trade-offs across episodes of selection and environments influence life-history evolution and adaptive population divergence. Documenting these trade-offs remains challenging as selection can vary in magnitude and direction through time and space. Here, we evaluate fitness trade-offs at the levels of the whole organism and the quantitative trait locus (QTL) in a multiyear field study of Boechera stricta (Brassicaceae), a genetically tractable mustard native to the Rocky Mountains. Reciprocal local adaptation was pronounced for viability, but not for reproductive components of fitness. Instead, local genomes had a fecundity advantage only in the high latitude garden. By estimating realized selection coefficients from individual-level data on viability and reproductive success and permuting the data to infer significance, we examined the genetic basis of fitness trade-offs. This analytical approach (Conditional Neutrality-Antagonistic Pleiotropy, CNAP) identified genetic trade-offs at a flowering phenology QTL (costs of adaptation) and revealed genetic trade-offs across fitness components (costs of reproduction). These patterns would not have emerged from traditional ANOVA-based QTL mapping. Our analytical framework can be applied to other systems to investigate fitness trade-offs. This task is becoming increasingly important as climate change may alter fitness landscapes, potentially disrupting fitness trade-offs that took many generations to evolve. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  8. Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children.

    PubMed

    Bauer, Tobias; Trump, Saskia; Ishaque, Naveed; Thürmann, Loreen; Gu, Lei; Bauer, Mario; Bieg, Matthias; Gu, Zuguang; Weichenhan, Dieter; Mallm, Jan-Philipp; Röder, Stefan; Herberth, Gunda; Takada, Eiko; Mücke, Oliver; Winter, Marcus; Junge, Kristin M; Grützmann, Konrad; Rolle-Kampczyk, Ulrike; Wang, Qi; Lawerenz, Christian; Borte, Michael; Polte, Tobias; Schlesner, Matthias; Schanne, Michaela; Wiemann, Stefan; Geörg, Christina; Stunnenberg, Hendrik G; Plass, Christoph; Rippe, Karsten; Mizuguchi, Junichiro; Herrmann, Carl; Eils, Roland; Lehmann, Irina

    2016-03-24

    Epigenetic mechanisms have emerged as links between prenatal environmental exposure and disease risk later in life. Here, we studied epigenetic changes associated with maternal smoking at base pair resolution by mapping DNA methylation, histone modifications, and transcription in expectant mothers and their newborn children. We found extensive global differential methylation and carefully evaluated these changes to separate environment associated from genotype-related DNA methylation changes. Differential methylation is enriched in enhancer elements and targets in particular "commuting" enhancers having multiple, regulatory interactions with distal genes. Longitudinal whole-genome bisulfite sequencing revealed that DNA methylation changes associated with maternal smoking persist over years of life. Particularly in children prenatal environmental exposure leads to chromatin transitions into a hyperactive state. Combined DNA methylation, histone modification, and gene expression analyses indicate that differential methylation in enhancer regions is more often functionally translated than methylation changes in promoters or non-regulatory elements. Finally, we show that epigenetic deregulation of a commuting enhancer targeting c-Jun N-terminal kinase 2 (JNK2) is linked to impaired lung function in early childhood. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  9. Strong selection genome-wide enhances fitness tradeoffs across environments and episodes of selection

    PubMed Central

    Anderson, Jill T.; Lee, Cheng-Ruei; Mitchell-Olds, Thomas

    2014-01-01

    Fitness tradeoffs across episodes of selection and environments influence life history evolution and adaptive population divergence. Documenting these tradeoffs remains challenging as selection can vary in magnitude and direction through time and space. Here, we evaluate fitness tradeoffs at the levels of the whole organism and the quantitative trait locus (QTL) in a multiyear field study of Boechera stricta (Brassicaceae), a genetically tractable mustard native to the Rocky Mountains. Reciprocal local adaptation was pronounced for viability, but not for reproductive components of fitness. Instead, local genomes had a fecundity advantage only in the high latitude garden. By estimating realized selection coefficients from individual level data on viability and reproductive success and permuting the data to infer significance, we examined the genetic basis of fitness tradeoffs. This analytical approach (Conditional Neutrality-Antagonistic Pleiotropy, CNAP) identified genetic tradeoffs at a flowering phenology QTL (costs of adaptation) and revealed genetic tradeoffs across fitness components (costs of reproduction). These patterns would not have emerged from traditional ANOVA-based QTL mapping. Our analytical framework can be applied to other systems to investigate fitness tradeoffs. This task is becoming increasingly important as climate change may alter fitness landscapes, potentially disrupting fitness tradeoffs that took many generations to evolve. PMID:24102539

  10. Non-genomic steroid actions in human spermatozoa. "Persistent tickling from a laden environment".

    PubMed

    Correia, Joao Natalino; Conner, Sarah J; Kirkman-Brown, Jackson C

    2007-05-01

    As sperm traverse the female tract from vagina to oocyte, they experience a steroid milieu, which due to transcriptional inactivity, they can only respond to via non-genomic signaling. This environment mediates events including capacitation, changes in motility patterns, chemotaxis, and acrosome reaction. Current knowledge of the events, calcium signaling pathways, and potential identity of receptors involved is reviewed in light of recent data, with a context for further work in the field, and emphasizing the importance of steroids as a mixed stimulant. Progesterone receptor candidates are considered in light of recent findings, including novel classes of receptors such as a progesterone membrane receptor component-1 or -2 complex with serpine-1 mRNA binding protein, the best candidate so far for progesterone activity in human sperm. Given the number of other alternative candidates and the apparent diversity of the signaling pathways activated, the presence of multiple species of progesterone receptors should not be excluded. Given that sperm dysfunction is the most common defined cause of infertility, advances in our currently limited knowledge of these pathways and events are crucial to not only create better therapies but also improve rational diagnosis.

  11. Comparative Functional Genomics of Lactobacillus spp. Reveals Possible Mechanisms for Specialization of Vaginal Lactobacilli to Their Environment

    PubMed Central

    Suzuki, Haruo; Hickey, Roxana J.; Forney, Larry J.

    2014-01-01

    Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either over- or underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species-specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health. PMID:24488312

  12. Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment.

    PubMed

    Mendes-Soares, Helena; Suzuki, Haruo; Hickey, Roxana J; Forney, Larry J

    2014-04-01

    Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either over- or underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species-specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health.

  13. Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis.

    PubMed

    Lowry, David B; Logan, Tierney L; Santuari, Luca; Hardtke, Christian S; Richards, James H; DeRose-Wilson, Leah J; McKay, John K; Sen, Saunak; Juenger, Thomas E

    2013-09-01

    The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.

  14. Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments.

    PubMed

    Bonnefoy, Violaine; Holmes, David S

    2012-07-01

    This minireview presents recent advances in our understanding of iron oxidation and homeostasis in acidophilic Bacteria and Archaea. These processes influence the flux of metals and nutrients in pristine and man-made acidic environments such as acid mine drainage and industrial bioleaching operations. Acidophiles are also being studied to understand life in extreme conditions and their role in the generation of biomarkers used in the search for evidence of existing or past extra-terrestrial life. Iron oxidation in acidophiles is best understood in the model organism Acidithiobacillus ferrooxidans. However, recent functional genomic analysis of acidophiles is leading to a deeper appreciation of the diversity of acidophilic iron-oxidizing pathways. Although it is too early to paint a detailed picture of the role played by lateral gene transfer in the evolution of iron oxidation, emerging evidence tends to support the view that iron oxidation arose independently more than once in evolution. Acidic environments are generally rich in soluble iron and extreme acidophiles (e.g. the Leptospirillum genus) have considerably fewer iron uptake systems compared with neutrophiles. However, some acidophiles have been shown to grow as high as pH 6 and, in the case of the Acidithiobacillus genus, to have multiple iron uptake systems. This could be an adaption allowing them to respond to different iron concentrations via the use of a multiplicity of different siderophores. Both Leptospirillum spp. and Acidithiobacillus spp. are predicted to synthesize the acid stable citrate siderophore for Fe(III) uptake. In addition, both groups have predicted receptors for siderophores produced by other microorganisms, suggesting that competition for iron occurs influencing the ecophysiology of acidic environments. Little is known about the genetic regulation of iron oxidation and iron uptake in acidophiles, especially how the use of iron as an energy source is balanced with its need to take up

  15. Specific Mg 2+ binding to AT-rich regions of chromatin in the evolution of eukaryotes

    NASA Astrophysics Data System (ADS)

    Strissel, P. L.; Gavrilov, K. L.; Levi-Setti, R.; Strick, R.

    2006-07-01

    At SIMS XIV, we reported SIMS evidence of specific Mg 2+ binding to the AT-rich regions of human metaphase chromosomes represented by G-bands. Subsequent Mg 2+-depletion experiments supported a direct role for Mg 2+ in promoting and maintaining the higher order chromatin structure originating G-bands, possibly due to both Mg 2+-DNA and Mg 2+-protein interactions. An in-depth study, reported elsewhere, implicated also Ca 2+ in the maintenance of chromatin ultrastructure in the scaffold of mammalian chromosomes, in association with topoisomerase II. We examine here the association of Mg 2+ with AT-rich regions of chromatin in the chromosomes of the Indian muntjac deer (IMD), leading to conclusions similar to the above. To answer the question whether the presumed divalent cation role in the chromosomes of advanced eukaryotes had an evolutionary history to be traced back to earlier evolutionary stages, we have SIMS-mapped Ca 2+ and Mg 2+ in BrdU-labeled polytene chromosomes from the salivary gland of the Dipteran Drosophila melanogaster. Striking Ca 2+ and Mg 2+ SIMS banding patterns correlating with those of the Br label (a thymidine analogue) implicate unequivocally a close association of both these cations with the AT-rich regions of DNA for these primitive eukaryotes.

  16. The Genome Sizes of Ostracod Crustaceans Correlate with Body Size and Evolutionary History, but not Environment.

    PubMed

    Jeffery, Nicholas W; Ellis, Emily A; Oakley, Todd H; Gregory, T Ryan

    2017-09-01

    Within animals, a positive correlation between genome size and body size has been detected in several taxa but not in others, such that it remains unknown how pervasive this pattern may be. Here, we provide another example of a positive relationship in a group of crustaceans whose genome sizes have not previously been investigated. We analyze genome size estimates for 46 species across the 2 most diverse orders of Class Ostracoda, commonly known as seed shrimps, including 29 new estimates made using Feulgen image analysis densitometry and flow cytometry. Genome sizes in this group range ~80-fold, a level of variability that is otherwise not seen in crustaceans with the exception of some malacostracan orders. We find a strong positive correlation between genome size and body size across all species, including after phylogenetic correction. We additionally detect evidence of XX/XO sex determination in 3 species of marine ostracods where male and female genome sizes were estimated. On average, genome sizes are larger but less variable in Order Myodocopida than in Order Podocopida, and marine ostracods have larger genomes than freshwater species, but this appears to be explained by phylogenetic inertia. The relationship between phylogeny, genome size, body size, and habitat is complex in this system and provides a baseline for future studies examining the interactions of these biological traits. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. AT-rich palindromes mediate the constitutional t(11;22) translocation.

    PubMed

    Edelmann, L; Spiteri, E; Koren, K; Pulijaal, V; Bialer, M G; Shanske, A; Goldberg, R; Morrow, B E

    2001-01-01

    The constitutional t(11;22) translocation is the only known recurrent non-Robertsonian translocation in humans. Offspring are susceptible to der(22) syndrome, a severe congenital anomaly disorder caused by 3&rcolon;1 meiotic nondisjunction events. We previously localized the t(11;22) translocation breakpoint to a region on 22q11 within a low-copy repeat termed "LCR22" and within an AT-rich repeat on 11q23. The LCR22s are implicated in mediating different rearrangements on 22q11, leading to velocardiofacial syndrome/DiGeorge syndrome and cat-eye syndrome by homologous recombination mechanisms. The LCR22s contain AT-rich repetitive sequences, suggesting that such repeats may mediate the t(11;22) translocation. To determine the molecular basis of the translocation, we cloned and sequenced the t(11;22) breakpoint in the derivative 11 and 22 chromosomes in 13 unrelated carriers, including two de novo cases and der(22) syndrome offspring. We found that, in all cases examined, the reciprocal exchange occurred between similar AT-rich repeats on both chromosomes 11q23 and 22q11. To understand the mechanism, we examined the sequence of the breakpoint intervals in the derivative chromosomes and compared this with the deduced normal chromosomal sequence. A palindromic AT-rich sequence with a near-perfect hairpin could form, by intrastrand base-pairing, on the parental chromosomes. The sequence of the breakpoint junction in both derivatives indicates that the exchange events occurred at the center of symmetry of the palindromes, and this resulted in small, overlapping staggered deletions in this region among the different carriers. On the basis of previous studies performed in diverse organisms, we hypothesize that double-strand breaks may occur in the center of the palindrome, the tip of the putative hairpin, leading to illegitimate recombination events between similar AT-rich sequences on chromosomes 11 and 22, resulting in deletions and loss of the palindrome, which then

  18. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

    PubMed

    Ferchaud, Anne-Laure; Hansen, Michael M

    2016-01-01

    Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the

  19. The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments

    PubMed Central

    Janssen, Paul J.; Van Houdt, Rob; Moors, Hugo; Monsieurs, Pieter; Morin, Nicolas; Michaux, Arlette; Benotmane, Mohammed A.; Leys, Natalie; Vallaeys, Tatiana; Lapidus, Alla; Monchy, Sébastien; Médigue, Claudine; Taghavi, Safiyh; McCorkle, Sean; Dunn, John; van der Lelie, Daniël; Mergeay, Max

    2010-01-01

    Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals. PMID:20463976

  20. The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Antropogenic Environments

    SciTech Connect

    Janssen, P.J.; van der Lelie, D.; Van Houdt, R.; Moors, H.; Monsieurs, P.; Morin, N.; Michaux, A.; Benotmane, M. A.; Leys, N.; Vallaeys, T.; Lapidus, A.; Monchy, S.; Medique, C.; Taghavi, S.; McCorkle, S.; Dunn, J.; Mergeay, M.

    2010-05-01

    Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.

  1. Genomic polymorphism and protein changes of soybean mutant induced by space environment

    NASA Astrophysics Data System (ADS)

    He, J.; Gao, Y.; Sun, Y.

    Soybean 194 4126 of excellent agricultural qualities such as high yield and rounder and wider leaf was selected in six generation after abroad recoverable satellite 15 days in 1996 from Soybean 72163 featured with long-leaf white-blossom grey-hair and infinitude-poding To explore the mechanisms of plant mutation induced by space environment we have experimented at genome and proteome level on Soybean 194 4126 and its control Soybean 72163 Amplified Fragment Length Polymorphism AFLP was used to identify mutated sits and the result shows that 36 polymorphic bands varying between 100 and 900 bp in 2022 DNA bands varying between 100 and 1500 bp have been amplified out of 64 pairs of primer combinations between mutant Soybean 194 4126 and the control plant So the mutation degree of DNA is 3 56 The protein two-dimensional electrophoresis 2-DE and peptide mass fingerprint PMF assays were used to investigate the difference of proteins in fruits and leaves between Soybean 194 4126 and its control Results indicate that 62 protein dots specially appear in Soybean 72163 and 39 dots specially in the mutant Soybean 194 4126 by image analysis software PDQuest in the 2-DE maps of soybean seeds Using PMF assay and protein data-base searching to investigate two distinct protein dots we found that the protein specially expressed in the seed of mutant Soybean 194 4126 may be Dehydrin and the other protein specially expressed in the seed of the control Soybean 72163 may be maturation-associated protein MAT1 Because Dehydrin and MAT1 are

  2. Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

    PubMed Central

    González, Josefa; Karasov, Talia L.; Messer, Philipp W.; Petrov, Dmitri A.

    2010-01-01

    Investigating spatial patterns of loci under selection can give insight into how populations evolved in response to selective pressures and can provide monitoring tools for detecting the impact of environmental changes on populations. Drosophila is a particularly good model to study adaptation to environmental heterogeneity since it is a tropical species that originated in sub-Saharan Africa and has only recently colonized the rest of the world. There is strong evidence for the adaptive role of Transposable Elements (TEs) in the evolution of Drosophila, and TEs might play an important role specifically in adaptation to temperate climates. In this work, we analyzed the frequency of a set of putatively adaptive and putatively neutral TEs in populations with contrasting climates that were collected near the endpoints of two known latitudinal clines in Australia and North America. The contrasting results obtained for putatively adaptive and putatively neutral TEs and the consistency of the patterns between continents strongly suggest that putatively adaptive TEs are involved in adaptation to temperate climates. We integrated information on population behavior, possible environmental selective agents, and both molecular and functional information of the TEs and their nearby genes to infer the plausible phenotypic consequences of these insertions. We conclude that adaptation to temperate environments is widespread in Drosophila and that TEs play a significant role in this adaptation. It is remarkable that such a diverse set of TEs located next to a diverse set of genes are consistently adaptive to temperate climate-related factors. We argue that reverse population genomic analyses, as the one described in this work, are necessary to arrive at a comprehensive picture of adaptation. PMID:20386746

  3. Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep-Subsurface Environment.

    PubMed

    Singh, Nitin K; Carlson, Courtney; Sani, Rajesh K; Venkateswaran, Kasthuri

    2017-06-01

    The whole-genome sequences of seven thermophiles that could grow at >55°C, but not at 37°C, were generated. These thermophilic bacteria will play a useful role as model microorganisms, and analyzing their genomes will help to understand the observed production of novel bioactive compounds, including thermozymes and macromolecules. Copyright © 2017 Singh et al.

  4. Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

    PubMed Central

    Zhou, Jun; Sugiyama, Yuzo; Nishimura, Osamu; Aizu, Tomoyuki; Toyoda, Atsushi; Fujiyama, Asao; Agata, Kiyokazu

    2012-01-01

    Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation. PMID:22432011

  5. Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence

    PubMed Central

    Kennedy, Sean P.; Ng, Wailap Victor; Salzberg, Steven L.; Hood, Leroy; DasSarma, Shiladitya

    2001-01-01

    The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character. PMID:11591641

  6. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.

    PubMed

    Kennedy, S P; Ng, W V; Salzberg, S L; Hood, L; DasSarma, S

    2001-10-01

    The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.

  7. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals.

    PubMed

    Romiguier, Jonathan; Ranwez, Vincent; Delsuc, Frédéric; Galtier, Nicolas; Douzery, Emmanuel J P

    2013-09-01

    Despite the rapid increase of size in phylogenomic data sets, a number of important nodes on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal tree is still a controversial issue. One difficulty lies in the pervasive phylogenetic conflicts among genes, with each one telling its own story, which may be reliable or not. Here, we identified a simple criterion, that is, the GC content, which substantially helps in determining which gene trees best reflect the species tree. We assessed the ability of 13,111 coding sequence alignments to correctly reconstruct the placental phylogeny. We found that GC-rich genes induced a higher amount of conflict among gene trees and performed worse than AT-rich genes in retrieving well-supported, consensual nodes on the placental tree. We interpret this GC effect mainly as a consequence of genome-wide variations in recombination rate. Indeed, recombination is known to drive GC-content evolution through GC-biased gene conversion and might be problematic for phylogenetic reconstruction, for instance, in an incomplete lineage sorting context. When we focused on the AT-richest fraction of the data set, the resolution level of the placental phylogeny was greatly increased, and a strong support was obtained in favor of an Afrotheria rooting, that is, Afrotheria as the sister group of all other placentals. We show that in mammals most conflicts among gene trees, which have so far hampered the resolution of the placental tree, are concentrated in the GC-rich regions of the genome. We argue that the GC content-because it is a reliable indicator of the long-term recombination rate-is an informative criterion that could help in identifying the most reliable molecular markers for species tree inference.

  8. Genome-environment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica.

    PubMed

    Pluess, Andrea R; Frank, Aline; Heiri, Caroline; Lalagüe, Hadrien; Vendramin, Giovanni G; Oddou-Muratorio, Sylvie

    2016-04-01

    The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome-environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural Fagus sylvatica populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150 m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC.

  9. Genome composition and phylogeny of microbes predict their co-occurrence in the environment

    PubMed Central

    2017-01-01

    The genomic information of microbes is a major determinant of their phenotypic properties, yet it is largely unknown to what extent ecological associations between different species can be explained by their genome composition. To bridge this gap, this study introduces two new genome-wide pairwise measures of microbe-microbe interaction. The first (genome content similarity index) quantifies similarity in genome composition between two microbes, while the second (microbe-microbe functional association index) summarizes the topology of a protein functional association network built for a given pair of microbes and quantifies the fraction of network edges crossing organismal boundaries. These new indices are then used to predict co-occurrence between reference genomes from two 16S-based ecological datasets, accounting for phylogenetic relatedness of the taxa. Phylogenetic relatedness was found to be a strong predictor of ecological associations between microbes which explains about 10% of variance in co-occurrence data, but genome composition was found to be a strong predictor as well, it explains up to 4% the variance in co-occurrence when all genomic-based indices are used in combination, even after accounting for evolutionary relationships between the species. On their own, the metrics proposed here explain a larger proportion of variance than previously reported more complex methods that rely on metabolic network comparisons. In summary, results of this study indicate that microbial genomes do indeed contain detectable signal of organismal ecology, and the methods described in the paper can be used to improve mechanistic understanding of microbe-microbe interactions. PMID:28152007

  10. Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment.

    PubMed

    Pal, Siddhartha; Kundu, Anirban; Banerjee, Tirtha Das; Mohapatra, Balaram; Roy, Ajoy; Manna, Riddha; Sar, Pinaki; Kazy, Sufia K

    2017-06-15

    Franconibacter pulveris strain DJ34, isolated from Duliajan oil fields, Assam, was characterized in terms of its taxonomic, metabolic and genomic properties. The bacterium showed utilization of diverse petroleum hydrocarbons and electron acceptors, metal resistance, and biosurfactant production. The genome (4,856,096bp) of this strain contained different genes related to the degradation of various petroleum hydrocarbons, metal transport and resistance, dissimilatory nitrate, nitrite and sulfite reduction, chemotaxy, biosurfactant synthesis, etc. Genomic comparison with other Franconibacter spp. revealed higher abundance of genes for cell motility, lipid transport and metabolism, transcription and translation in DJ34 genome. Detailed COG analysis provides deeper insights into the genomic potential of this organism for degradation and survival in oil-contaminated complex habitat. This is the first report on ecophysiology and genomic inventory of Franconibacter sp. inhabiting crude oil rich environment, which might be useful for designing the strategy for bioremediation of oil contaminated environment. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Fragment Screening of Infectious Disease Targets in a Structural Genomics Environment

    PubMed Central

    Begley, Darren W; Davies, Douglas R; Hartley, Robert; Edwards, Thomas E; Staker, Bart L; Van Voorhis, Wesley C; Myler, Peter J; Stewart, Lance J

    2015-01-01

    Structural genomics efforts have traditionally focused on generating single protein structures of unique and diverse targets. However, a lone structure for a given target is often insufficient to firmly assign function or to drive drug discovery. As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to expand the focus of structural genomics by elucidating ensembles of structures that examine small molecule-protein interactions for selected infectious disease targets. In this chapter, we discuss two applications for small molecule libraries in structural genomics: unbiased fragment screening to provide inspiration for lead development, and targeted, knowledge-based screening to confirm or correct the functional annotation of a given gene product. This shift in emphasis results in a structural genomics effort that is more engaged with the infectious disease research community, and one that produces structures of greater utility to researchers interested in both protein function and inhibitor development. We also describe specific methods for conducting high-throughput fragment screening in a structural genomics context by X-ray crystallography. PMID:21371605

  12. Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment.

    PubMed

    Snauwaert, Isabel; Stragier, Pieter; De Vuyst, Luc; Vandamme, Peter

    2015-04-03

    Pediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions. It proved to be capable of growing in beer, thereby resisting this environment, which is unfavorable for microbial growth. The molecular mechanisms underlying its metabolic capabilities and niche adaptations were unknown up to now. In the present study, whole-genome sequencing and comparative genome analysis were used to investigate this strain's mechanisms to reside in the beer niche, with special focus on not only stress and hop resistances but also folate biosynthesis and exopolysaccharide (EPS) production. The draft genome sequence of P. damnosus LMG 28219 harbored 183 contigs, including an intact prophage region and several coding sequences involved in plasmid replication. The annotation of 2178 coding sequences revealed the presence of many transporters and transcriptional regulators and several genes involved in oxidative stress response, hop resistance, de novo folate biosynthesis, and EPS production. Comparative genome analysis of P. damnosus LMG 28219 with Pediococcus claussenii ATCC BAA-344(T) (beer origin) and Pediococcus pentosaceus ATCC 25745 (plant origin) revealed that various hop resistance genes and genes involved in de novo folate biosynthesis were unique to the strains isolated from beer. This contrasted with the genes related to osmotic stress responses, which were shared between the strains compared. Furthermore, transcriptional regulators were enriched in the genomes of bacteria capable of growth in beer, suggesting that those cause rapid up- or down-regulation of gene expression. Genome sequence analysis of P. damnosus LMG 28219 provided insights into the underlying mechanisms of its adaptation to the beer niche. The results presented will enable analysis of the transcriptome and proteome of P. damnosus LMG 28219, which will result in additional knowledge on its metabolic activities.

  13. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment.

    PubMed

    Kvitek, Daniel J; Sherlock, Gavin

    2013-11-01

    Molecular signaling networks are ubiquitous across life and likely evolved to allow organisms to sense and respond to environmental change in dynamic environments. Few examples exist regarding the dispensability of signaling networks, and it remains unclear whether they are an essential feature of a highly adapted biological system. Here, we show that signaling network function carries a fitness cost in yeast evolving in a constant environment. We performed whole-genome, whole-population Illumina sequencing on replicate evolution experiments and find the major theme of adaptive evolution in a constant environment is the disruption of signaling networks responsible for regulating the response to environmental perturbations. Over half of all identified mutations occurred in three major signaling networks that regulate growth control: glucose signaling, Ras/cAMP/PKA and HOG. This results in a loss of environmental sensitivity that is reproducible across experiments. However, adaptive clones show reduced viability under starvation conditions, demonstrating an evolutionary tradeoff. These mutations are beneficial in an environment with a constant and predictable nutrient supply, likely because they result in constitutive growth, but reduce fitness in an environment where nutrient supply is not constant. Our results are a clear example of the myopic nature of evolution: a loss of environmental sensitivity in a constant environment is adaptive in the short term, but maladaptive should the environment change.

  14. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses.

    PubMed

    Diemer, Geoffrey S; Stedman, Kenneth M

    2012-06-11

    Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.

  15. Pseudomonas lini Strain ZBG1 Revealed Carboxylic Acid Utilization and Copper Resistance Features Required for Adaptation to Vineyard Soil Environment: A Draft Genome Analysis

    PubMed Central

    Chan, Kok-Gan; Chong, Teik-Min; Adrian, Tan-Guan-Sheng; Kher, Heng Leong; Grandclément, Catherine; Faure, Denis; Yin, Wai-Fong; Dessaux, Yves; Hong, Kar-Wai

    2016-01-01

    Pseudomonas lini strain ZBG1 was isolated from the soil of vineyard in Zellenberg, France and the draft genome was reported in this study. Bioinformatics analyses of the genome revealed presence of genes encoding tartaric and malic acid utilization as well as copper resistance that correspond to the adaptation this strain in vineyard soil environment. PMID:27512520

  16. Succession of Phylogeny and Function During Plant Litter Decomposition (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Brodie, Eoin

    2013-03-01

    Eoin Brodie of Berkeley Lab on "Succession of phylogeny and function during plant litter decomposition" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  17. Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Plant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Larsen, Peter

    2013-03-01

    Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  18. Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Gordon, Sean

    2013-03-01

    Sean Gordon of the USDA on "Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  19. Modulation of Root Microbiome Community Assembly by the Plant Immune Response (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Lebeis, Sarah

    2013-03-01

    Sarah Lebeis of University of North Carolina on "Modulation of root microbiome community assembly by the plant immune response" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  20. Metabolic Engineering of Clostridium thermocellum for Biofuel Production (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Guess, Adam

    2013-03-01

    Adam Guss of Oak Ridge National Lab on "Metabolic engineering of Clostridium thermocellum for biofuel production" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  1. Biodiversity Monitoring Using NGS Approaches on Unusual Substrates (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Gilbert, Tom

    2013-03-01

    Tom Gilbert of the Natural History Museum of Denmark on "Biodiversity monitoring using NGS approaches on unusual substrates" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  2. Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Hibbett, David [Clark University

    2016-07-12

    David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  3. Draft Genome Sequence of Bacillus selenatarsenatis SF-1T, a Promising Agent for Bioremediation of Environments Contaminated with Selenium and Arsenic

    PubMed Central

    Kuroda, Masashi; Ayano, Hiroyuki; Sei, Kazunari; Yamashita, Mitsuo

    2015-01-01

    Bacillus selenatarsenatis sp. nov. strain SF-1T is a promising agent for bioremediation of environments contaminated with selenium and arsenic. Here, we report the draft genome sequence of this strain. PMID:25614571

  4. Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Hazen, Sam

    2013-03-01

    Sam Hazen of the University of Massachusetts on "Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  5. Draft Genome Sequence of Bacillus selenatarsenatis SF-1T, a Promising Agent for Bioremediation of Environments Contaminated with Selenium and Arsenic.

    PubMed

    Kuroda, Masashi; Ayano, Hiroyuki; Sei, Kazunari; Yamashita, Mitsuo; Ike, Michihiko

    2015-01-22

    Bacillus selenatarsenatis sp. nov. strain SF-1(T) is a promising agent for bioremediation of environments contaminated with selenium and arsenic. Here, we report the draft genome sequence of this strain. Copyright © 2015 Kuroda et al.

  6. TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Karsenti, Eric

    2013-03-01

    Eric Karsenti of EMBL delivers the closing keynote on "TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  7. Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Hibbett, David

    2012-03-21

    David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  8. Assembly-driven metagenomics of a hypersaline microbial ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Allen, Eric

    2013-03-01

    Eric Allen of Scripps and UC San Diego on "Assembly-driven metagenomics of a hypersaline microbial ecosystem" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  9. Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment

    PubMed Central

    Lucchetti-Miganeh, Céline; Redelberger, David; Chambonnier, Gaël; Rechenmann, François; Elsen, Sylvie; Bordi, Christophe; Jeannot, Katy; Attrée, Ina; Plésiat, Patrick; de Bentzmann, Sophie

    2014-01-01

    Pseudomonas aeruginosa is a Gram-negative environmental species and an opportunistic microorganism, establishing itself in vulnerable patients, such as those with cystic fibrosis (CF) or those hospitalized in intensive care units (ICU). It has become a major cause of nosocomial infections worldwide and a serious threat to Public Health because of overuse and misuse of antibiotics that have selected highly resistant strains against which very few therapeutic options exist. Herein is illustrated the intraclonal evolution of the genome of sequential isolates collected in a single CF patient from the early phase of pulmonary colonization to the fatal outcome. We also examined at the whole genome scale a pair of genotypically-related strains made of a drug susceptible, environmental isolate recovered from an ICU sink and of its multidrug resistant counterpart found to infect an ICU patient. Multiple genetic changes accumulated in the CF isolates over the disease time course including SNPs, deletion events and reduction of whole genome size. The strain isolated from the ICU patient displayed an increase in the genome size of 4.8% with major genetic rearrangements as compared to the initial environmental strain. The annotated genomes are given in free access in an interactive web application WallGene designed to facilitate large-scale comparative analysis and thus allowing investigators to explore homologies and syntenies between P. aeruginosa strains, here PAO1 and the five clinical strains described. PMID:25437802

  10. Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

    PubMed

    Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

    2015-01-01

    Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

  11. Genome sequencing and analysis of a highly virulent Vibrio parahaemolyticus strain isolated from the marine environment

    NASA Astrophysics Data System (ADS)

    Parks, M. C.; Moreno, E.

    2016-02-01

    Vibrio parahaemolyticus [Vp] is a Gram-negative bacterium and a natural inhabitant of coastal marine ecosystems worldwide. Vp is also a coincidental pathogen of humans. Virulent strains are commonly identified by the presence of the thermostable direct (tdh) or tdh-related (trh) hemolysin genes. However, virulence is multifaceted and many clinical Vp isolates do not carry tdh or trh. In this study, we sequenced and assembled the draft genome of a tdh- and trh-negative environmental isolate (805) shown previously to be highly virulent in zebrafish. To investigate potential mechanisms of virulence, we compared 805 to the clinical V. parahaemolyticus type strain (RIMD2210633). Pairwise comparison revealed the presence of multiple genomic regions including an IncF conjugative pilus (1.3 Kb) and a colicin V plasmid (1.49 Kb). These features are homologous to genomic regions present in clinical V. vulnificus and V. cholerae strains. Genome comparison also revealed the presence of five toxin-antitoxin systems. Isolate 805 likely attained these new features through the lateral acquisition of mobile genomic material - a hypothesis supported by the aberrant GC content of these regions. Colicin V plasmids are a diverse group of IncF plasmids found in invasive bacterial strains. Similarly, an abundance of toxin-antitoxin systems have been linked to virulence in Gram-negative bacteria. Current efforts are focused on characterizing 142 coding features present in 805 but absent from the type strain.

  12. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

    PubMed Central

    2010-01-01

    Background The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium. Results The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes. Conclusions These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria. PMID:21167037

  13. Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes.

    PubMed

    Nirea, K G; Meuwissen, T H E

    2017-04-01

    We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross-breed. Elite nucleus herds had access to high-quality feed, and production herds were fed low-quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (rg  = 0.2), medium (rg  = 0.5) and high (rg  = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high-density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40-115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high-quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43-104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population.

  14. Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments.

    PubMed

    Tobler, Ray; Franssen, Susanne U; Kofler, Robert; Orozco-Terwengel, Pablo; Nolte, Viola; Hermisson, Joachim; Schlötterer, Christian

    2014-02-01

    Experimental evolution in combination with whole-genome sequencing (evolve and resequence [E&R]) is a promising approach to define the genotype-phenotype map and to understand adaptation in evolving populations. Many previous studies have identified a large number of putative selected sites (i.e., candidate loci), but it remains unclear to what extent these loci are genuine targets of selection or experimental noise. To address this question, we exposed the same founder population to two different selection regimes-a hot environment and a cold environment-and quantified the genomic response in each. We detected large numbers of putative selected loci in both environments, albeit with little overlap between the two sets of candidates, indicating that most resulted from habitat-specific selection. By quantifying changes across multiple independent biological replicates, we demonstrate that most of the candidate SNPs were false positives that were linked to selected sites over distances much larger than the typical linkage disequilibrium range of Drosophila melanogaster. We show that many of these mid- to long-range associations were attributable to large segregating inversions and confirm by computer simulations that such patterns could be readily replicated when strong selection acts on rare haplotypes. In light of our findings, we outline recommendations to improve the performance of future Drosophila E&R studies which include using species with negligible inversion loads, such as D. mauritiana and D. simulans, instead of D. melanogaster.

  15. The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element.

    PubMed

    Dinh, Thanh Theresa; Girke, Thomas; Liu, Xigang; Yant, Levi; Schmid, Markus; Chen, Xuemei

    2012-06-01

    Cell fate specification in development requires transcription factors for proper regulation of gene expression. In Arabidopsis, transcription factors encoded by four classes of homeotic genes, A, B, C and E, act in a combinatorial manner to control proper floral organ identity. The A-class gene APETALA2 (AP2) promotes sepal and petal identities in whorls 1 and 2 and restricts the expression of the C-class gene AGAMOUS (AG) from whorls 1 and 2. However, it is unknown how AP2 performs these functions. Unlike the other highly characterized floral homeotic proteins containing MADS domains, AP2 has two DNA-binding domains referred to as the AP2 domains and its DNA recognition sequence is still unknown. Here, we show that the second AP2 domain in AP2 binds a non-canonical AT-rich target sequence, and, using a GUS reporter system, we demonstrate that the presence of this sequence in the AG second intron is important for the restriction of AG expression in vivo. Furthermore, we show that AP2 binds the AG second intron and directly regulates AG expression through this sequence element. Computational analysis reveals that the binding site is highly conserved in the second intron of AG orthologs throughout Brassicaceae. By uncovering a biologically relevant AT-rich target sequence, this work shows that AP2 domains have wide-ranging target specificities and provides a missing link in the mechanisms that underlie flower development. It also sets the foundation for understanding the basis of the broad biological functions of AP2 in Arabidopsis, as well as the divergent biological functions of AP2 orthologs in dicotyledonous plants.

  16. Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece.

    PubMed

    Castillo, Daniel; Jun, Jin Woo; D'Alvise, Paul; Middelboe, Mathias; Gram, Lone; Liu, Siyang; Katharios, Pantelis

    2015-07-02

    Vibrio parahaemolyticus is an important foodborne pathogen responsible for gastroenteritis outbreaks globally. It has also been identified as an important pathogen in aquatic organisms. Here, we report a draft genome sequence of V. parahaemolyticus, strain VH3, isolated from farmed juvenile greater amberjack, Seriola dumerili, in Greece. Copyright © 2015 Castillo et al.

  17. Complete Genome Sequences of Three Cupriavidus Strains Isolated from Various Malaysian Environments

    PubMed Central

    Shafie, Nur Asilla Hani; Lau, Nyok-Sean; Ramachandran, Hema

    2017-01-01

    ABSTRACT Cupriavidus sp. USMAA1020, USMAA2-4, and USMAHM13 are capable of producing polyhydroxyalkanoate (PHA). This biopolymer is an alternative solution to synthetic plastics, whereby polyhydroxyalkanoate synthase is the key enzyme involved in PHA biosynthesis. Here, we report the complete genomes of three Cupriavidus sp. strains: USMAA1020, USMAA2-4, and USMAHM13. PMID:28104662

  18. Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments

    USDA-ARS?s Scientific Manuscript database

    Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date and anthesis-silking interva...

  19. Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece

    PubMed Central

    Castillo, Daniel; Jun, Jin Woo; D’Alvise, Paul; Middelboe, Mathias; Gram, Lone; Liu, Siyang

    2015-01-01

    Vibrio parahaemolyticus is an important foodborne pathogen responsible for gastroenteritis outbreaks globally. It has also been identified as an important pathogen in aquatic organisms. Here, we report a draft genome sequence of V. parahaemolyticus, strain VH3, isolated from farmed juvenile greater amberjack, Seriola dumerili, in Greece. PMID:26139725

  20. Using genomic prediction to characterize environments and optimize prediction accuracy in applied breeding data

    USDA-ARS?s Scientific Manuscript database

    Simulation and empirical studies of genomic selection (GS) show accuracies sufficient to generate rapid annual genetic gains. It also shifts the focus from the evaluation of lines to the evaluation of alleles. Consequently, new methods should be developed to optimize the use of large historic multi-...

  1. Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption

    PubMed Central

    2015-01-01

    Objective Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. Methods To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Results Our solution supports evaluation of the D′ measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. Conclusions With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical. PMID:26732892

  2. Analysis of bacterial populations in the environment using two-dimensional gel electrophoresis of genomic DNA and complementary DNA.

    PubMed

    Liu, Guo-Hua; Nakamura, Tatsuo; Amemiya, Takashi; Rajendran, Narasimmalu; Itoh, Kiminori

    2011-01-01

    Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.

  3. Special AT-rich sequence-binding protein 2 acts as a negative regulator of stemness in colorectal cancer cells

    PubMed Central

    Li, Ying; Liu, Yu-Hong; Hu, Yu-Ying; Chen, Lin; Li, Jian-Ming

    2016-01-01

    AIM To find the mechanisms by which special AT-rich sequence-binding protein 2 (SATB2) influences colorectal cancer (CRC) metastasis. METHODS Cell growth assay, colony-forming assay, cell adhesion assay and cell migration assay were used to evaluate the biological characteristics of CRC cells with gain or loss of SATB2. Sphere formation assay was used to detect the self-renewal ability of CRC cells. The mRNA expression of stem cell markers in CRC cells with upregulated or downregulated SATB2 expression was detected by quantitative real-time polymerase chain reaction. Chromatin immunoprecipitation (ChIP) was used to verify the binding loci of SATB2 on genomic sequences of stem cell markers. The Cancer Genome Atlas (TCGA) database and our clinical samples were analyzed to find the correlation between SATB2 and some key stem cell markers. RESULTS Downregulation of SATB2 led to an aggressive phenotype in SW480 and DLD-1 cells, which was characterized by increased migration and invasion abilities. Overexpression of SATB2 suppressed the migration and invasion abilities in SW480 and SW620 cells. Using sequential sphere formation assay to detect the self-renewal abilities of CRC cells, we found more secondary sphere formation but not primary sphere formation in SW480 and DLD-1 cells after SATB2 expression was knocked down. Moreover, most markers for stem cells such as CD133, CD44, AXIN2, MEIS2 and NANOG were increased in cells with SATB2 knockdown and decreased in cells with SATB2 overexpression. ChIP assay showed that SATB2 bound to regulatory elements of CD133, CD44, MEIS2 and AXIN2 genes. Using TCGA database and our clinical samples, we found that SATB2 was correlated with some key stem cell markers including CD44 and CD24 in clinical tissues of CRC patients. CONCLUSION SATB2 can directly bind to the regulatory elements in the genetic loci of several stem cell markers and consequently inhibit the progression of CRC by negatively regulating stemness of CRC cells. PMID

  4. FW: An R Package for Finlay-Wilkinson Regression that Incorporates Genomic/Pedigree Information and Covariance Structures Between Environments.

    PubMed

    Lian, Lian; de Los Campos, Gustavo

    2015-12-29

    The Finlay-Wilkinson regression (FW) is a popular method among plant breeders to describe genotype by environment interaction. The standard implementation is a two-step procedure that uses environment (sample) means as covariates in a within-line ordinary least squares (OLS) regression. This procedure can be suboptimal for at least four reasons: (1) in the first step environmental means are typically estimated without considering genetic-by-environment interactions, (2) in the second step uncertainty about the environmental means is ignored, (3) estimation is performed regarding lines and environment as fixed effects, and (4) the procedure does not incorporate genetic (either pedigree-derived or marker-derived) relationships. Su et al. proposed to address these problems using a Bayesian method that allows simultaneous estimation of environmental and genotype parameters, and allows incorporation of pedigree information. In this article we: (1) extend the model presented by Su et al. to allow integration of genomic information [e.g., single nucleotide polymorphism (SNP)] and covariance between environments, (2) present an R package (FW) that implements these methods, and (3) illustrate the use of the package using examples based on real data. The FW R package implements both the two-step OLS method and a full Bayesian approach for Finlay-Wilkinson regression with a very simple interface. Using a real wheat data set we demonstrate that the prediction accuracy of the Bayesian approach is consistently higher than the one achieved by the two-step OLS method. Copyright © 2016 Lian and Campos.

  5. A Bayesian Poisson-lognormal Model for Count Data for Multiple-Trait Multiple-Environment Genomic-Enabled Prediction

    PubMed Central

    Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H.; Montesinos-López, José C.; Singh, Pawan; Juliana, Philomin; Salinas-Ruiz, Josafhat

    2017-01-01

    When a plant scientist wishes to make genomic-enabled predictions of multiple traits measured in multiple individuals in multiple environments, the most common strategy for performing the analysis is to use a single trait at a time taking into account genotype × environment interaction (G × E), because there is a lack of comprehensive models that simultaneously take into account the correlated counting traits and G × E. For this reason, in this study we propose a multiple-trait and multiple-environment model for count data. The proposed model was developed under the Bayesian paradigm for which we developed a Markov Chain Monte Carlo (MCMC) with noninformative priors. This allows obtaining all required full conditional distributions of the parameters leading to an exact Gibbs sampler for the posterior distribution. Our model was tested with simulated data and a real data set. Results show that the proposed multi-trait, multi-environment model is an attractive alternative for modeling multiple count traits measured in multiple environments. PMID:28364037

  6. A Bayesian Poisson-lognormal Model for Count Data for Multiple-Trait Multiple-Environment Genomic-Enabled Prediction.

    PubMed

    Montesinos-López, Osval A; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H; Montesinos-López, José C; Singh, Pawan; Juliana, Philomin; Salinas-Ruiz, Josafhat

    2017-05-05

    When a plant scientist wishes to make genomic-enabled predictions of multiple traits measured in multiple individuals in multiple environments, the most common strategy for performing the analysis is to use a single trait at a time taking into account genotype × environment interaction (G × E), because there is a lack of comprehensive models that simultaneously take into account the correlated counting traits and G × E. For this reason, in this study we propose a multiple-trait and multiple-environment model for count data. The proposed model was developed under the Bayesian paradigm for which we developed a Markov Chain Monte Carlo (MCMC) with noninformative priors. This allows obtaining all required full conditional distributions of the parameters leading to an exact Gibbs sampler for the posterior distribution. Our model was tested with simulated data and a real data set. Results show that the proposed multi-trait, multi-environment model is an attractive alternative for modeling multiple count traits measured in multiple environments. Copyright © 2017 Montesinos-López et al.

  7. Integrating genomics and transcriptomics with geo-ethnicity and the environment for the resolution of complex cardiovascular diseases.

    PubMed

    Seda, Ondrej; Tremblay, Johanne; Sedová, Lucie; Hamet, Pavel

    2005-12-01

    One of the crucial steps on the way to individualized medicine to treat cardiovascular disease (CVD) is to better understand the identities, roles, extent and at least the major patterns of interaction between influential genomic and environmental factors. It is clear that such a bold goal can hardly be achieved without a major upgrade of our conceptualization of the phenomena studied, taking advantage of recent developments of novel technological and computational tools. Firstly, the search for the genomic components of the most common multifactorial CVDs is no longer restricted to protein-coding genes; truly genome-wide investigations should replace them in both humans and animal models. Secondly, the 'environment' has also undergone semantic expansion, incorporating such remote constituents as developmental plasticity and epigenetics on one side, and socioeconomic status on the other. To elucidate and analyze the resulting complex picture, appropriate statistical models and approaches need to be designed to tackle issues such as population stratification and admixture, multiple testing, and multidimensionality reduction in models involving multiple genes and environmental factors. Eventually, an integrated platform bringing together all of the above will probably be necessary to secure relevant information specific to a particular combination of conditions and settings (age, geo-ethnicity and exposure), which may perhaps become visible only after a step back, through systems (network) biology.

  8. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments.

    PubMed

    Varshney, Rajeev K; Shi, Chengcheng; Thudi, Mahendar; Mariac, Cedric; Wallace, Jason; Qi, Peng; Zhang, He; Zhao, Yusheng; Wang, Xiyin; Rathore, Abhishek; Srivastava, Rakesh K; Chitikineni, Annapurna; Fan, Guangyi; Bajaj, Prasad; Punnuri, Somashekhar; Gupta, S K; Wang, Hao; Jiang, Yong; Couderc, Marie; Katta, Mohan A V S K; Paudel, Dev R; Mungra, K D; Chen, Wenbin; Harris-Shultz, Karen R; Garg, Vanika; Desai, Neetin; Doddamani, Dadakhalandar; Kane, Ndjido Ardo; Conner, Joann A; Ghatak, Arindam; Chaturvedi, Palak; Subramaniam, Sabarinath; Yadav, Om Parkash; Berthouly-Salazar, Cécile; Hamidou, Falalou; Wang, Jianping; Liang, Xinming; Clotault, Jérémy; Upadhyaya, Hari D; Cubry, Philippe; Rhoné, Bénédicte; Gueye, Mame Codou; Sunkar, Ramanjulu; Dupuy, Christian; Sparvoli, Francesca; Cheng, Shifeng; Mahala, R S; Singh, Bharat; Yadav, Rattan S; Lyons, Eric; Datta, Swapan K; Hash, C Tom; Devos, Katrien M; Buckler, Edward; Bennetzen, Jeffrey L; Paterson, Andrew H; Ozias-Akins, Peggy; Grando, Stefania; Wang, Jun; Mohapatra, Trilochan; Weckwerth, Wolfram; Reif, Jochen C; Liu, Xin; Vigouroux, Yves; Xu, Xun

    2017-09-18

    Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

  9. Metingear: a development environment for annotating genome-scale metabolic models.

    PubMed

    May, John W; James, A Gordon; Steinbeck, Christoph

    2013-09-01

    Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format. Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.

  10. The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

    PubMed Central

    2013-01-01

    Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world’s terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind. PMID:23940263

  11. The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.

    PubMed

    2013-01-01

    Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.

  12. Draft Genome Sequences of Four Thermophilic Spore Formers Isolated from a Dairy-Processing Environment

    PubMed Central

    Caspers, Martien P. M.; Boekhorst, Jos; de Jong, Anne; Kort, Remco; Nierop Groot, Masja

    2016-01-01

    Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy products. Here, we report draft genome sequences of four thermophilic strains from a milk-processing plant or standard milk, namely, a Geobacillus thermoglucosidans isolate (TNO-09.023), Geobacillus stearothermophilus TNO-09.027, and two Anoxybacillus flavithermus isolates (TNO-09.014 and TNO-09.016). PMID:27516503

  13. Genome anchored QTLs for biomass productivity in Hybrid Populus: Heterosis and detection across Contrasting Environments.

    SciTech Connect

    Muchero, Wellington; Sewell, Mitchell; Gunter, Lee E; Tschaplinski, Timothy J; Yin, Tongming; DiFazio, Steven P; Tuskan, Gerald A

    2013-01-01

    Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in an interspecific F2 population derived from an outbred Populus trichocarpa P. deltoides parental cross. Three years of phenotypic data for stem growth traits (height and diameter) were collected from two parental, two F1 and 339 F2 trees in a clonal trial replicated both within and among two environmentally contrasting sites in the North American Pacific Northwest. A genetic linkage map comprised of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring QTL using the Multiple-QTL Model (MQM) package of the statistical program MapQTL 6. A total of twelve QTLs, nine putative and three suggestive, were identified with eight of these being identified at both sites in at least one experiment. Of these, three putative QTL BM-1, BM-2, BM-7, on LGs I, II, and XIV, respectively, were identified in all three years for both height and diameter. Two QTLs BM-2 and BM-7, on LG II and XIV, respectively, exhibited significant evidence of over-dominance in all three years for both traits. Conversely a QTL on BM-6 LG XIII exhibited out-breeding depression in two years for both height and diameter. The remaining nine QTLs showed difference levels of dominance and additive effects. Seven of the nine QTL were successfully anchored and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions positions. QTL BM-7 on LG XIV had been anchored on the genome assembly in a previous study, therefore eight QTLs identified in this study were assigned genome assembly positions. Physical distances encompassed by each QTL regions ranged from 1.3 to 8.8 Mb.

  14. Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD-9.

    PubMed

    Goh, Yong Jun; Goin, Caitlin; O'Flaherty, Sarah; Altermann, Eric; Hutkins, Robert

    2011-08-30

    Streptococcus thermophilus represents the only species among the streptococci that has "Generally Regarded As Safe" status and that plays an economically important role in the fermentation of yogurt and cheeses. We conducted comparative genome analysis of S. thermophilus LMD-9 to identify unique gene features as well as features that contribute to its adaptation to the dairy environment. In addition, we investigated the transcriptome response of LMD-9 during growth in milk in the presence of Lactobacillus delbrueckii ssp. bulgaricus, a companion culture in yogurt fermentation, and during lytic bacteriophage infection. The S. thermophilus LMD-9 genome is comprised of a 1.8 Mbp circular chromosome (39.1% GC; 1,834 predicted open reading frames) and two small cryptic plasmids. Genome comparison with the previously sequenced LMG 18311 and CNRZ1066 strains revealed 114 kb of LMD-9 specific chromosomal region, including genes that encode for histidine biosynthetic pathway, a cell surface proteinase, various host defense mechanisms and a phage remnant. Interestingly, also unique to LMD-9 are genes encoding for a putative mucus-binding protein, a peptide transporter, and exopolysaccharide biosynthetic proteins that have close orthologs in human intestinal microorganisms. LMD-9 harbors a large number of pseudogenes (13% of ORFeome), indicating that like LMG 18311 and CNRZ1066, LMD-9 has also undergone major reductive evolution, with the loss of carbohydrate metabolic genes and virulence genes found in their streptococcal counterparts. Functional genome distribution analysis of ORFeomes among streptococci showed that all three S. thermophilus strains formed a distinct functional cluster, further establishing their specialized adaptation to the nutrient-rich milk niche. An upregulation of CRISPR1 expression in LMD-9 during lytic bacteriophage DT1 infection suggests its protective role against phage invasion. When co-cultured with L. bulgaricus, LMD-9 overexpressed genes

  15. Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD-9

    PubMed Central

    2011-01-01

    Background Streptococcus thermophilus represents the only species among the streptococci that has “Generally Regarded As Safe” status and that plays an economically important role in the fermentation of yogurt and cheeses. We conducted comparative genome analysis of S. thermophilus LMD-9 to identify unique gene features as well as features that contribute to its adaptation to the dairy environment. In addition, we investigated the transcriptome response of LMD-9 during growth in milk in the presence of Lactobacillus delbrueckii ssp. bulgaricus, a companion culture in yogurt fermentation, and during lytic bacteriophage infection. Results The S. thermophilus LMD-9 genome is comprised of a 1.8 Mbp circular chromosome (39.1% GC; 1,834 predicted open reading frames) and two small cryptic plasmids. Genome comparison with the previously sequenced LMG 18311 and CNRZ1066 strains revealed 114 kb of LMD-9 specific chromosomal region, including genes that encode for histidine biosynthetic pathway, a cell surface proteinase, various host defense mechanisms and a phage remnant. Interestingly, also unique to LMD-9 are genes encoding for a putative mucus-binding protein, a peptide transporter, and exopolysaccharide biosynthetic proteins that have close orthologs in human intestinal microorganisms. LMD-9 harbors a large number of pseudogenes (13% of ORFeome), indicating that like LMG 18311 and CNRZ1066, LMD-9 has also undergone major reductive evolution, with the loss of carbohydrate metabolic genes and virulence genes found in their streptococcal counterparts. Functional genome distribution analysis of ORFeomes among streptococci showed that all three S. thermophilus strains formed a distinct functional cluster, further establishing their specialized adaptation to the nutrient-rich milk niche. An upregulation of CRISPR1 expression in LMD-9 during lytic bacteriophage DT1 infection suggests its protective role against phage invasion. When co-cultured with L. bulgaricus, LMD-9

  16. Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the Arctic environment

    USGS Publications Warehouse

    Welch, Andreanna J.; Bedoya-Reina, Oscar C.; Carretero-Paulet, Lorenzo; Miller, Webb; Rode, Karyn D.; Lindqvist, Charlotte

    2014-01-01

    Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate if polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex, and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide, which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of nitric oxide as an adaptive response to control trade-offs between energy production in the form of ATP versus generation of heat (thermogenesis).

  17. Polar Bears Exhibit Genome-Wide Signatures of Bioenergetic Adaptation to Life in the Arctic Environment

    PubMed Central

    Welch, Andreanna J.; Carretero-Paulet, Lorenzo; Miller, Webb; Rode, Karyn D.; Lindqvist, Charlotte

    2014-01-01

    Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate whether polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide (NO), which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of NO as an adaptive response to control trade-offs between energy production in the form of adenosine triphosphate versus generation of heat (thermogenesis). PMID:24504087

  18. Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments.

    PubMed

    Windhausen, Vanessa S; Atlin, Gary N; Hickey, John M; Crossa, Jose; Jannink, Jean-Luc; Sorrells, Mark E; Raman, Babu; Cairns, Jill E; Tarekegne, Amsal; Semagn, Kassa; Beyene, Yoseph; Grudloyma, Pichet; Technow, Frank; Riedelsheimer, Christian; Melchinger, Albrecht E

    2012-11-01

    Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F(2)-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F(2)-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set.

  19. Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment.

    PubMed

    Welch, Andreanna J; Bedoya-Reina, Oscar C; Carretero-Paulet, Lorenzo; Miller, Webb; Rode, Karyn D; Lindqvist, Charlotte

    2014-02-01

    Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate whether polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide (NO), which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of NO as an adaptive response to control trade-offs between energy production in the form of adenosine triphosphate versus generation of heat (thermogenesis).

  20. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.

    PubMed

    Ino, Kohei; Hernsdorf, Alex W; Konno, Uta; Kouduka, Mariko; Yanagawa, Katsunori; Kato, Shingo; Sunamura, Michinari; Hirota, Akinari; Togo, Yoko S; Ito, Kazumasa; Fukuda, Akari; Iwatsuki, Teruki; Mizuno, Takashi; Komatsu, Daisuke D; Tsunogai, Urumu; Ishimura, Toyoho; Amano, Yuki; Thomas, Brian C; Banfield, Jillian F; Suzuki, Yohey

    2017-09-08

    Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with (13)C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.The ISME Journal advance online publication, 8 September 2017; doi:10.1038/ismej.2017.140.

  1. Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

    DOE PAGES

    Browne, Patrick; Tamaki, Hideyuki; Kyrpides, Nikos; ...

    2016-08-23

    Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H 2 -CO 2 utilizing) methanoarchaea in a broad range of anoxic habitats. In spite of their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centeredmore » on improved transport of scarce inorganic nutrients and likely use H + rather than Na + transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na + and H + chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, our findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.« less

  2. Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments

    PubMed Central

    Windhausen, Vanessa S.; Atlin, Gary N.; Hickey, John M.; Crossa, Jose; Jannink, Jean-Luc; Sorrells, Mark E.; Raman, Babu; Cairns, Jill E.; Tarekegne, Amsal; Semagn, Kassa; Beyene, Yoseph; Grudloyma, Pichet; Technow, Frank; Riedelsheimer, Christian; Melchinger, Albrecht E.

    2012-01-01

    Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F2-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F2-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set. PMID:23173094

  3. Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

    SciTech Connect

    Browne, Patrick; Tamaki, Hideyuki; Kyrpides, Nikos; Woyke, Tanja; Goodwin, Lynne; Imachi, Hiroyuki; Bräuer, Suzanna; Yavitt, Joseph B.; Liu, Wen-Tso; Zinder, Stephen; Cadillo-Quiroz, Hinsby

    2016-08-23

    Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H 2 -CO 2 utilizing) methanoarchaea in a broad range of anoxic habitats. In spite of their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H + rather than Na + transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na + and H + chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, our findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

  4. Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment

    PubMed Central

    Thomas, Torsten; Evans, Flavia F.; Schleheck, David; Mai-Prochnow, Anne; Burke, Catherine; Penesyan, Anahit; Dalisay, Doralyn S.; Stelzer-Braid, Sacha; Saunders, Neil; Johnson, Justin; Ferriera, Steve; Kjelleberg, Staffan; Egan, Suhelen

    2008-01-01

    Background Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. Methodology/Principal Findings To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. Conclusions/Significance The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community

  5. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

    PubMed Central

    2012-01-01

    Background Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Results Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. Conclusions This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. Reviewers This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section. PMID:22515485

  6. Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.

    PubMed

    Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

    2016-03-01

    Although genome-wide association studies (GWASs) have discovered numerous novel genetic variants associated with many complex traits and diseases, those genetic variants typically explain only a small fraction of phenotypic variance. Factors that account for phenotypic variance include environmental factors and gene-by-environment interactions (GEIs). Recently, several studies have conducted genome-wide gene-by-environment association analyses and demonstrated important roles of GEIs in complex traits. One of the main challenges in these association studies is to control effects of population structure that may cause spurious associations. Many studies have analyzed how population structure influences statistics of genetic variants and developed several statistical approaches to correct for population structure. However, the impact of population structure on GEI statistics in GWASs has not been extensively studied and nor have there been methods designed to correct for population structure on GEI statistics. In this paper, we show both analytically and empirically that population structure may cause spurious GEIs and use both simulation and two GWAS datasets to support our finding. We propose a statistical approach based on mixed models to account for population structure on GEI statistics. We find that our approach effectively controls population structure on statistics for GEIs as well as for genetic variants.

  7. Evolution of Hsp70 Gene Expression: A Role for Changes in AT-Richness within Promoters

    PubMed Central

    Ma, Ronghui; Zhang, Bo; Kang, Le

    2011-01-01

    In disparate organisms adaptation to thermal stress has been linked to changes in the expression of genes encoding heat-shock proteins (Hsp). The underlying genetics, however, remain elusive. We show here that two AT-rich sequence elements in the promoter region of the hsp70 gene of the fly Liriomyza sativae that are absent in the congeneric species, Liriomyza huidobrensis, have marked cis-regulatory consequences. We studied the cis-regulatory consequences of these elements (called ATRS1 and ATRS2) by measuring the constitutive and heat-shock-induced luciferase luminescence that they drive in cells transfected with constructs carrying them modified, deleted, or intact, in the hsp70 promoter fused to the luciferase gene. The elements affected expression level markedly and in different ways: Deleting ATRS1 augmented both the constitutive and the heat-shock-induced luminescence, suggesting that this element represses transcription. Interestingly, replacing the element with random sequences of the same length and A+T content delivered the wild-type luminescence pattern, proving that the element's high A+T content is crucial for its effects. Deleting ATRS2 decreased luminescence dramatically and almost abolished heat-shock inducibility and so did replacing the element with random sequences matching the element's length and A+T content, suggesting that ATRS2's effects on transcription and heat-shock inducibility involve a common mechanism requiring at least in part the element's specific primary structure. Finally, constitutive and heat-shock luminescence were reduced strongly when two putative binding sites for the Zeste transcription factor identified within ATRS2 were altered through site-directed mutagenesis, and the heat-shock-induced luminescence increased when Zeste was over-expressed, indicating that Zeste participates in the effects mapped to ATRS2 at least in part. AT-rich sequences are common in promoters and our results suggest that they should play important

  8. Evolution of hsp70 gene expression: a role for changes in AT-richness within promoters.

    PubMed

    Chen, Bing; Jia, Tieliu; Ma, Ronghui; Zhang, Bo; Kang, Le

    2011-01-01

    In disparate organisms adaptation to thermal stress has been linked to changes in the expression of genes encoding heat-shock proteins (Hsp). The underlying genetics, however, remain elusive. We show here that two AT-rich sequence elements in the promoter region of the hsp70 gene of the fly Liriomyza sativae that are absent in the congeneric species, Liriomyza huidobrensis, have marked cis-regulatory consequences. We studied the cis-regulatory consequences of these elements (called ATRS1 and ATRS2) by measuring the constitutive and heat-shock-induced luciferase luminescence that they drive in cells transfected with constructs carrying them modified, deleted, or intact, in the hsp70 promoter fused to the luciferase gene. The elements affected expression level markedly and in different ways: Deleting ATRS1 augmented both the constitutive and the heat-shock-induced luminescence, suggesting that this element represses transcription. Interestingly, replacing the element with random sequences of the same length and A+T content delivered the wild-type luminescence pattern, proving that the element's high A+T content is crucial for its effects. Deleting ATRS2 decreased luminescence dramatically and almost abolished heat-shock inducibility and so did replacing the element with random sequences matching the element's length and A+T content, suggesting that ATRS2's effects on transcription and heat-shock inducibility involve a common mechanism requiring at least in part the element's specific primary structure. Finally, constitutive and heat-shock luminescence were reduced strongly when two putative binding sites for the Zeste transcription factor identified within ATRS2 were altered through site-directed mutagenesis, and the heat-shock-induced luminescence increased when Zeste was over-expressed, indicating that Zeste participates in the effects mapped to ATRS2 at least in part. AT-rich sequences are common in promoters and our results suggest that they should play important

  9. Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami.

    PubMed

    Hiraoka, Satoshi; Machiyama, Asako; Ijichi, Minoru; Inoue, Kentaro; Oshima, Kenshiro; Hattori, Masahira; Yoshizawa, Susumu; Kogure, Kazuhiro; Iwasaki, Wataru

    2016-01-14

    The Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil. As expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experiments confirmed weak cultivability of some of these strains in iron-limited media. Furthermore, metagenomic analyses demonstrated over-representation of denitrification-related genes in the tsunami-affected soil sample, as well as the presence of pathogenic and marine-living genera and genes related to salt-tolerance. Collectively, the present results would provide an example of microbial characteristics of soil disturbed by the tsunami, which may give an insight into microbial adaptation to drastic environmental changes. Further analyses on microbial ecology after a tsunami are envisioned to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems.

  10. Genomic Prediction of Genotypic Effects with Epistasis and Environment Interactions for Yield-Related Traits of Rapeseed (Brassica napus L.)

    PubMed Central

    Luo, Xiang; Ding, Yi; Zhang, Linzhong; Yue, Yao; Snyder, John H.; Ma, Chaozhi; Zhu, Jun

    2017-01-01

    Oilseed rape (Brassica napus) is an economically important oil crop, yet the genetic architecture of its complex traits remain largely unknown. Here, genome-wide association study was conducted for eight yield-related traits to dissect the genetic architecture of additive, dominance, epistasis, and their environment interaction. Additionally, the optimal genotype combination and the breeding value of superior line, superior hybrid and existing best line in mapping population were predicted for each trait in two environments based on the predicted genotypic effects. As a result, 17 quantitative trait SNPs (QTSs) were identified significantly for target traits with total heritability varied from 58.47 to 87.98%, most of which were contributed by dominance, epistasis, and environment-specific effects. The results indicated that non-additive effects were large contributions to heritability and epistasis, and also noted that environment interactions were important variants for oilseed breeding. Our study facilitates the understanding of genetic basis of rapeseed yield trait, helps to accelerate rapeseed breading, and also offers a roadmap for precision plant breeding via marker-assisted selection. PMID:28270831

  11. The little bacteria that can – diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

    PubMed Central

    Taş, Neslihan; Van Eekert, Miriam H. A.; De Vos, Willem M.; Smidt, Hauke

    2010-01-01

    Summary The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments. PMID:21255338

  12. Genomic analysis of Ascochyta rabiei identifies dynamic genome environments of solanapyrone biosynthesis gene cluster and a novel type of pathway-specific regulator

    USDA-ARS?s Scientific Manuscript database

    Secondary metabolite genes are often clustered together and situated in particular genomic regions such as the subtelomere, which can facilitate niche adaptation in fungi. Solanapyrones are toxic secondary metabolites produced by fungi occupying different ecological niches. Full genome sequencing of...

  13. Gene-environment interaction effects on lung function- a genome-wide association study within the Framingham heart study

    PubMed Central

    2013-01-01

    Background Previous studies in occupational exposure and lung function have focused only on the main effect of occupational exposure or genetics on lung function. Some disease-susceptible genes may be missed due to their low marginal effects, despite potential involvement in the disease process through interactions with the environment. Through comprehensive genome-wide gene-environment interaction studies, we can uncover these susceptibility genes. Our objective in this study was to explore gene by occupational exposure interaction effects on lung function using both the individual SNPs approach and the genetic network approach. Methods The study population comprised the Offspring Cohort and the Third Generation from the Framingham Heart Study. We used forced expiratory volume in one second (FEV1) and ratio of FEV1 to forced vital capacity (FVC) as outcomes. Occupational exposures were classified using a population-specific job exposure matrix. We performed genome-wide gene-environment interaction analysis, using the Affymetrix 550 K mapping array for genotyping. A linear regression-based generalized estimating equation was applied to account for within-family relatedness. Network analysis was conducted using results from single-nucleotide polymorphism (SNP)-level analyses and from gene expression study results. Results There were 4,785 participants in total. SNP-level analysis and network analysis identified SNP rs9931086 (Pinteraction =1.16 × 10-7) in gene SLC38A8, which may significantly modify the effects of occupational exposure on FEV1. Genes identified from the network analysis included CTLA-4, HDAC, and PPAR-alpha. Conclusions Our study implies that SNP rs9931086 in SLC38A8 and genes CTLA-4, HDAC, and PPAR-alpha, which are related to inflammatory processes, may modify the effect of occupational exposure on lung function. PMID:24289273

  14. Metingear: a development environment for annotating genome-scale metabolic models

    PubMed Central

    May, John W.; James, A. Gordon; Steinbeck, Christoph

    2013-01-01

    Summary: Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format. Availability: Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X. Contact: johnmay@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23766418

  15. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

    PubMed Central

    2011-01-01

    Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and

  16. Latency Entry of Herpes Simplex Virus 1 Is Determined by the Interaction of Its Genome with the Nuclear Environment

    PubMed Central

    Cohen, Camille; Streichenberger, Nathalie; Texier, Pascale; Takissian, Julie; Rousseau, Antoine; Poccardi, Nolwenn; Welsch, Jérémy; Corpet, Armelle; Schaeffer, Laurent; Labetoulle, Marc; Lomonte, Patrick

    2016-01-01

    Herpes simplex virus 1 (HSV-1) establishes latency in trigeminal ganglia (TG) sensory neurons of infected individuals. The commitment of infected neurons toward the viral lytic or latent transcriptional program is likely to depend on both viral and cellular factors, and to differ among individual neurons. In this study, we used a mouse model of HSV-1 infection to investigate the relationship between viral genomes and the nuclear environment in terms of the establishment of latency. During acute infection, viral genomes show two major patterns: replication compartments or multiple spots distributed in the nucleoplasm (namely “multiple-acute”). Viral genomes in the “multiple-acute” pattern are systematically associated with the promyelocytic leukemia (PML) protein in structures designated viral DNA-containing PML nuclear bodies (vDCP-NBs). To investigate the viral and cellular features that favor the acquisition of the latency-associated viral genome patterns, we infected mouse primary TG neurons from wild type (wt) mice or knock-out mice for type 1 interferon (IFN) receptor with wt or a mutant HSV-1, which is unable to replicate due to the synthesis of a non-functional ICP4, the major virus transactivator. We found that the inability of the virus to initiate the lytic program combined to its inability to synthesize a functional ICP0, are the two viral features leading to the formation of vDCP-NBs. The formation of the “multiple-latency” pattern is favored by the type 1 IFN signaling pathway in the context of neurons infected by a virus able to replicate through the expression of a functional ICP4 but unable to express functional VP16 and ICP0. Analyses of TGs harvested from HSV-1 latently infected humans showed that viral genomes and PML occupy similar nuclear areas in infected neurons, eventually forming vDCP-NB-like structures. Overall our study designates PML protein and PML-NBs to be major cellular components involved in the control of HSV-1 latency

  17. Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri.

    PubMed

    Barbosa, Beathriz G V; Fernandez-García, Laura; Gato, Eva; López, Maria; Blasco, Lucia; Leão, Robson Souza; Albano, Rodolpho M; Fernández, Begoña; Cuenca, Felipe-Fernández; Pascual, Álvaro; Bou, German; Marques, Elizabeth A; Tomás, María

    2016-12-08

    Acinetobacter spp. are found in 53% of air colonization samples from the hospital environment. In this work, we sequenced all the genome of airborne Acinetobacter sp. strain 5-2Ac02. We found important features at the genomic level in regards to the rhizome. By phylogenetic analysis, A. towneri was the species most closely related to Acinetobacter sp. 5-2Ac02. Copyright © 2016 Barbosa et al.

  18. Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri

    PubMed Central

    Barbosa, Beathriz G. V.; Fernandez-García, Laura; Gato, Eva; López, Maria; Blasco, Lucia; Leão, Robson Souza; Albano, Rodolpho M.; Fernández, Begoña; Cuenca, Felipe-Fernández; Pascual, Álvaro; Bou, German; Marques, Elizabeth A.

    2016-01-01

    Acinetobacter spp. are found in 53% of air colonization samples from the hospital environment. In this work, we sequenced all the genome of airborne Acinetobacter sp. strain 5-2Ac02. We found important features at the genomic level in regards to the rhizome. By phylogenetic analysis, A. towneri was the species most closely related to Acinetobacter sp. 5-2Ac02. PMID:27932646

  19. Gene-Environment Interactions in Genome-Wide Association Studies: Current Approaches and New Directions

    ERIC Educational Resources Information Center

    Winham, Stacey J.; Biernacka, Joanna M.

    2013-01-01

    Background: Complex psychiatric traits have long been thought to be the result of a combination of genetic and environmental factors, and gene-environment interactions are thought to play a crucial role in behavioral phenotypes and the susceptibility and progression of psychiatric disorders. Candidate gene studies to investigate hypothesized…

  20. Gene-Environment Interactions in Genome-Wide Association Studies: Current Approaches and New Directions

    ERIC Educational Resources Information Center

    Winham, Stacey J.; Biernacka, Joanna M.

    2013-01-01

    Background: Complex psychiatric traits have long been thought to be the result of a combination of genetic and environmental factors, and gene-environment interactions are thought to play a crucial role in behavioral phenotypes and the susceptibility and progression of psychiatric disorders. Candidate gene studies to investigate hypothesized…

  1. Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis.

    PubMed

    Naj, Adam C; Scott, William K; Courtenay, Monique D; Cade, William H; Schwartz, Stephen G; Kovach, Jaclyn L; Agarwal, Anita; Wang, Gaofeng; Haines, Jonathan L; Pericak-Vance, Margaret A

    2013-05-01

    Relatively little is known about the interaction between genes and environment in the complex etiology of age-related macular degeneration (AMD). This study aimed to identify novel factors associated with AMD by analyzing gene-smoking interactions in a genome-wide association study of 1207 AMD cases and 686 controls of Caucasian background with genotype data on 668,238 single nucleotide polymorphisms (SNPs) after quality control. Participants' history of smoking at least 100 cigarettes lifetime was determined by a self-administered questionnaire. SNP associations modeled the effect of the minor allele additively on AMD using logistic regression, with adjustment for age, sex, and ever/never smoking. Joint effects of SNPs and smoking were examined comparing a null model containing only age, sex, and smoking against an extended model including genotypic and interaction terms. Genome-wide significant main effects were detected at three known AMD loci: CFH (P = 7.51×10(-30) ), ARMS2 (P = 1.94×10(-23) ), and RDBP/CFB/C2 (P = 4.37×10(-10) ), while joint effects analysis revealed three genomic regions with P < 10(-5) . Analyses stratified by smoking found genetic associations largely restricted to nonsmokers, with one notable exception: the chromosome 18q22.1 intergenic SNP rs17073641 (between SERPINB8 and CDH7), more strongly associated in nonsmokers (OR = 0.57, P = 2.73 × 10(-5) ), with an inverse association among smokers (OR = 1.42, P = 0.00228), suggesting that smoking modifies the effect of some genetic polymorphisms on AMD risk.

  2. Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment

    PubMed Central

    Rotman, Ella; Kouzminova, Elena; Plunkett, Guy

    2012-01-01

    The novel temperate bacteriophage Lula, contaminating laboratory Escherichia coli strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering an E. coli-toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage's damL gene, coding for DNA adenine methylase, did not make DNA cuttable. The damL mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the host dam mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene, dinL. We found that dinL mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80, gamL, encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote, agt, apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens are recD and sbcCD phenocopies, so GamL and Agt are part of lysogenic conversion. PMID:23042999

  3. Isolation by environment in White-breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach.

    PubMed

    Manthey, Joseph D; Moyle, Robert G

    2015-07-01

    Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE - disentangled from IBD - in sky island vertebrates and identify potential adaptive genetic variation.

  4. Genomic Prediction with Pedigree and Genotype × Environment Interaction in Spring Wheat Grown in South and West Asia, North Africa, and Mexico

    PubMed Central

    Sukumaran, Sivakumar; Crossa, Jose; Jarquin, Diego; Lopes, Marta; Reynolds, Matthew P.

    2016-01-01

    Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV) scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a subset of lines that were not observed in any of the 18 environments (CV1), and a subset of lines that were not observed in a set of the environments, but were observed in other environments (CV2). Genomic prediction models, including genotype × environment (G×E) interaction, had the highest average prediction ability under the CV1 scenario for GY (0.31), GN (0.32), GW (0.45), and TTF (0.27). For CV2, the average prediction ability of the model including the interaction terms was generally high for GY (0.38), GN (0.43), GW (0.63), and TTF (0.53). Wheat lines in site-year combinations in Mexico and India had relatively high prediction ability for GY and GW. Results indicated that prediction ability of lines not observed in certain environments could be relatively high for genomic selection when predicting G×E interaction in multi-environment trials. PMID:27903632

  5. Genomic Prediction with Pedigree and Genotype × Environment Interaction in Spring Wheat Grown in South and West Asia, North Africa, and Mexico.

    PubMed

    Sukumaran, Sivakumar; Crossa, Jose; Jarquin, Diego; Lopes, Marta; Reynolds, Matthew P

    2017-02-09

    Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV) scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a subset of lines that were not observed in any of the 18 environments (CV1), and a subset of lines that were not observed in a set of the environments, but were observed in other environments (CV2). Genomic prediction models, including genotype × environment (G×E) interaction, had the highest average prediction ability under the CV1 scenario for GY (0.31), GN (0.32), GW (0.45), and TTF (0.27). For CV2, the average prediction ability of the model including the interaction terms was generally high for GY (0.38), GN (0.43), GW (0.63), and TTF (0.53). Wheat lines in site-year combinations in Mexico and India had relatively high prediction ability for GY and GW. Results indicated that prediction ability of lines not observed in certain environments could be relatively high for genomic selection when predicting G×E interaction in multi-environment trials.

  6. Is the gene-environment interaction paradigm relevant to genome-wide studies? The case of education and body mass index.

    PubMed

    Boardman, Jason D; Domingue, Benjamin W; Blalock, Casey L; Haberstick, Brett C; Harris, Kathleen Mullan; McQueen, Matthew B

    2014-02-01

    This study uses data from the Framingham Heart Study to examine the relevance of the gene-environment interaction paradigm for genome-wide association studies (GWAS). We use completed college education as our environmental measure and estimate the interactive effect of genotype and education on body mass index (BMI) using 260,402 single-nucleotide polymorphisms (SNPs). Our results highlight the sensitivity of parameter estimates obtained from GWAS models and the difficulty of framing genome-wide results using the existing gene-environment interaction typology. We argue that SNP-environment interactions across the human genome are not likely to provide consistent evidence regarding genetic influences on health that differ by environment. Nevertheless, genome-wide data contain rich information about individual respondents, and we demonstrate the utility of this type of data. We highlight the fact that GWAS is just one use of genome-wide data, and we encourage demographers to develop methods that incorporate this vast amount of information from respondents into their analyses.

  7. Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

    PubMed Central

    Oliver, Haley F.; Wiedmann, Martin; den Bakker, Henk C.

    2015-01-01

    While the food-borne pathogen Listeria monocytogenes can persist in food associated environments, there are no whole-genome sequence (WGS) based methods to differentiate persistent from sporadic strains. Whole-genome sequencing of 188 isolates from a longitudinal study of L. monocytogenes in retail delis was used to (i) apply single-nucleotide polymorphism (SNP)-based phylogenetics for subtyping of L. monocytogenes, (ii) use SNP counts to differentiate persistent from repeatedly reintroduced strains, and (iii) identify genetic determinants of L. monocytogenes persistence. WGS analysis revealed three prophage regions that explained differences between three pairs of phylogenetically similar populations with pulsed-field gel electrophoresis types that differed by ≤3 bands. WGS-SNP-based phylogenetics found that putatively persistent L. monocytogenes represent SNP patterns (i) unique to a single retail deli, supporting persistence within the deli (11 clades), (ii) unique to a single state, supporting clonal spread within a state (7 clades), or (iii) spanning multiple states (5 clades). Isolates that formed one of 11 deli-specific clades differed by a median of 10 SNPs or fewer. Isolates from 12 putative persistence events had significantly fewer SNPs (median, 2 to 22 SNPs) than between isolates of the same subtype from other delis (median up to 77 SNPs), supporting persistence of the strain. In 13 events, nearly indistinguishable isolates (0 to 1 SNP) were found across multiple delis. No individual genes were enriched among persistent isolates compared to sporadic isolates. Our data show that WGS analysis improves food-borne pathogen subtyping and identification of persistent bacterial pathogens in food associated environments. PMID:26116683

  8. A genomic study on mammary gland acclimatization to tropical environment in the Holstein cattle.

    PubMed

    Wetzel-Gastal, D; Feitor, F; van Harten, S; Sebastiana, M; Sousa, L M R; Cardoso, L A

    2017-09-27

    This study aims at identifying mammary gland genes expressed in Brazilian Holstein cattle produced under tropical conditions, as compared to the Portuguese Holstein cattle produced in a temperate region. For this purpose, cDNA microarrays and real-time (RT) PCR transcriptomic techniques were utilized in 12 Holstein cows from the same lactating phase and management systems divided into two groups: Holstein Brazil (HB) originated from Brazil and Holstein Portugal (HP) from Portugal. The genomic results show that from a total of 4608 genes available from the microarray slide (Bovine Long Oligo (BLO) library), 65 transcripts were identified as differentially expressed in mammary glands. The genes associated with mammary gland development and heat stress responses showed greater expression in HB animals. In the HP group, upregulated genes related with apoptosis and vascular development and downregulated genes related with resistance to heat stress were observed. Validation of microarray results was done using RT-PCR. HB animals had higher blood levels of growth hormone than HP animals. Blood levels of prolactin and T3 were similar for both groups and GH levels were increased in the HB group. The results suggest a gene change towards long-term acclimatization of Brazilian Holstein cattle to cope with tropical heat stress conditions.

  9. Isolation of genomic DNA suitable for community analysis from mature trees adapted to arid environment.

    PubMed

    Gupta, Amit Kumar; Harish; Rai, Manoj Kumar; Phulwaria, Mahendra; Shekhawat, Narpat Singh

    2011-11-10

    Isolation of intact and pure genomic DNA (gDNA) is essential for many molecular biology applications. It is difficult to isolate pure DNA from mature trees of hot and dry desert regions because of the accumulation of high level of polysaccharides, phenolic compounds, tannins etc. We hereby report the standardized protocol for the isolation and purification of gDNA from seven ecologically and medically important tree species of Combretaceae viz. Anogeissus (Anogeissus sericea var. nummularia, Anogeissus pendula, and Anogeissus latifolia) and Terminalia (Terminalia arjuna, Terminalia bellirica, Terminalia catappa and Terminalia chebula). This method involves (i) washing the sample twice with Triton buffer (2%) then (ii) isolation of gDNA by modified-CTAB (cetyl trimethyl ammonium bromide) method employing a high concentration (4%) of PVP (Polyvinylpyrrolidone) and 50mM ascorbic acid, and (iii) purification of this CTAB-isolated gDNA by spin-column. gDNA isolated by modified CTAB or spin-column alone were not found suitable for PCR amplification. The Triton washing step is also critical. The quality of DNA was determined by the A(260)/A(280) absorbance ratio. gDNA was also observed for its intactness by running on 0.8% agarose gel. The suitability of extracted DNA for PCR was tested by amplification with RAPD primers, which was successful. Further, rbcLa (barcoding gene) was amplified and sequenced to check the quality of extracted gDNA for its downstream applications.

  10. Caenorhabditis elegans Genomic Response to Soil Bacteria Predicts Environment-Specific Genetic Effects on Life History Traits

    PubMed Central

    Coolon, Joseph D.; Jones, Kenneth L.; Todd, Timothy C.; Carr, Bryanua C.; Herman, Michael A.

    2009-01-01

    With the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. One application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. These experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. However, whether differential expression is predictive of functional importance has yet to be tested. Here we have addressed this expectation by employing Caenorhabditis elegans as a model for the interaction of native soil nematode taxa and soil bacteria. Using transcriptional profiling, we identified candidate genes regulated in response to different bacteria isolated in association with grassland nematodes or from grassland soils. Many of the regulated candidate genes are predicted to affect metabolism and innate immunity suggesting similar genes could influence nematode community dynamics in natural systems. Using mutations that inactivate 21 of the identified genes, we showed that most contribute to lifespan and/or fitness in a given bacterial environment. Although these bacteria may not be natural food sources for C. elegans, we show that changes in food source, as can occur in environmental disturbance, can have a large effect on gene expression, with important consequences for fitness. Moreover, we used regression analysis to demonstrate that for many genes the degree of differential gene expression between two bacterial environments predicted the magnitude of the effect of the loss of gene function on life history traits in those environments. PMID:19503598

  11. Allowing for population stratification in case-only studies of gene-environment interaction, using genomic control.

    PubMed

    Yadav, Pankaj; Freitag-Wolf, Sandra; Lieb, Wolfgang; Dempfle, Astrid; Krawczak, Michael

    2015-10-01

    Gene-environment interactions (G × E) have attracted considerable research interest in the past owing to their scientific and public health implications, but powerful statistical methods are required to successfully track down G × E, particularly at a genome-wide level. Previously, a case-only (CO) design has been proposed as a means to identify G × E with greater efficiency than traditional case-control or cohort studies. However, as with genotype-phenotype association studies themselves, hidden population stratification (PS) can impact the validity of G × E studies using a CO design. Since this problem has been subject to little research to date, we used comprehensive simulation to systematically assess the type I error rate, power and effect size bias of CO studies of G × E in the presence of PS. Three types of PS were considered, namely genetic-only (PSG), environment-only (PSE), and joint genetic and environmental stratification (PSGE). Our results reveal that the type I error rate of an unadjusted Wald test, appropriate for the CO design, would be close to its nominal level (0.05 in our study) as long as PS involves only one interaction partner (i.e., either PSG or PSE). In contrast, if the study population is stratified with respect to both G and E (i.e., if there is PSGE), then the type I error rate is seriously inflated and estimates of the underlying G × E interaction are biased. Comparison of CO to a family-based case-parents design confirmed that the latter is more robust against PSGE, as expected. However, case-parent trios may be particularly unsuitable for G × E studies in view of the fact that they require genotype data from parents and that many diseases with an environmental component are likely to be of late onset. An alternative approach to adjusting for PS is principal component analysis (PCA), which has been widely used for this very purpose in past genome-wide association studies (GWAS). However, resolving genetic PS properly by PCA

  12. Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle.

    PubMed

    Zhang, Li; Wang, Xiaolei; Yu, Min; Qiao, Yanlu; Zhang, Xiao-Hua

    2015-12-21

    Luteimonas abyssi XH031(T), which was previously isolated from subseafloor environment of the South Pacific Gyre (SPG), was an aerobic, gram-negative bacterium, and was identified to be a novel species of the genus Luteimonas in the family of Xanthomonadaceae. The nutrients utilization and metabolic mechanisms of XH031(T) indicate its plasticity. In view of the above characteristics, its genome was sequenced, and an in-depth analysis of the XH031(T) genome was performed to elucidate its adaption to extreme ecological environment. Various macromolecules including polysaccharide, protein, lipid and DNA could be degraded at low temperature by XH031(T) under laboratory conditions, and its degradation abilities to starch, gelatin and casein were considerably strong. Genome sequence analysis indicated that XH031(T) possesses extensive enzyme-encoding genes compared with four other Luteimonas strains. In addition, intricate systems (such as two-component regulatory systems, secretion systems, etc.), which are often used by bacteria to modulate the interactions of bacteria with their environments, were predicted in the genome of XH031(T). Genes encoding a choline-glycine betaine transporter and 99 extracellular peptidases featured with halophilicity were predicted in the genome, which might help the bacterium to adapt to the salty marine environment. Moreover, there were many gene clusters in the genome encoding ATP-binding cassette superfamily transporters, major facilitator superfamily transporters and cytochrome P450s that might function in the process of various substrate transportation and metabolisms. Furthermore, drug resistance genes harbored in the genome might signify that XH031(T) has evolved hereditary adaptation to toxic environment. Finally, the annotation of metabolic pathways of the elements (such as carbon, nitrogen, sulfur, phosphor and iron) in the genome elucidated the degradation of organic matter in the deep sediment of the SPG. The genome analysis

  13. Genes and environment - striking the fine balance between sophisticated biomonitoring and true functional environmental genomics.

    PubMed

    Steinberg, Christian E W; Stürzenbaum, Stephen R; Menzel, Ralph

    2008-08-01

    This article provides an overview how the application of the gene profiling (mainly via microarray technology) can be used in different organisms to address issues of environmental importance. Only recently, environmental sciences, including ecotoxicology, and molecular biology have started to mutually fertilize each other. This conceptual blend has enabled the identification of the interaction between molecular events and whole animal and population responses. Likewise, striking the fine balance between biomonitoring and functional environmental genomics will allow legislative and administrative measures to be based on a more robust platform. The application of DNA microarrays to ecotoxicogenomics links ecotoxicological effects of exposure with expression profiles of several thousand genes. The gene expression profiles are altered during toxicity, as either a direct or indirect result of toxicant exposure and the comparison of numerous specific expression profiles facilitates the differentiation between intoxication and true responses to environmental stressors. Furthermore, the application of microarrays provides the means to identify complex pathways and strategies that an exposed organism applies in response to environmental stressors. This review will present evidence that the widespread phenomenon of hormesis has a genetic basis that goes beyond an adaptive response. Some more practical advantages emerge: the toxicological assessment of complex mixtures, such as effluents or sediments, as well as drugs seems feasible, especially when classical ecotoxicological tests have failed. The review of available information demonstrates the advantages of microarray application to environmental issues spanning from bacteria, over algae and spermatophytes, to invertebrates (nematode Caenorhabditis elegans, crustacea Daphnia spp., earthworms), and various fish species. Microarrays have also highlighted why populations of a given species respond differently to similar

  14. Effects of Space Environment on Genome, Transcriptome, and Proteome of Klebsiella pneumoniae.

    PubMed

    Guo, Yinghua; Li, Jia; Liu, Jinwen; Wang, Tong; Li, Yinhu; Yuan, Yanting; Zhao, Jiao; Chang, De; Fang, Xiangqun; Li, Tianzhi; Wang, Junfeng; Dai, Wenkui; Fang, Chengxiang; Liu, Changting

    2015-11-01

    The aim of this study was to explore the effects of space flight on Klebsiella pneumoniae. A strain of K. pneumoniae was sent to space for 398 h aboard the ShenZhou VIII spacecraft during November 1, 2011-November 17, 2011. At the same time, a ground simulation with similar temperature conditions during the space flight was performed as a control. After the space mission, the flight and control strains were analyzed using phenotypic, genomic, transcriptomic and proteomic techniques. The flight strains LCT-KP289 exhibited a higher cotrimoxazole resistance level and changes in metabolism relative to the ground control strain LCT-KP214. After the space flight, 73 SNPs and a plasmid copy number variation were identified in the flight strain. Based on the transcriptomic analysis, there are 232 upregulated and 1879 downregulated genes, of which almost all were for metabolism. Proteomic analysis revealed that there were 57 upregulated and 125 downregulated proteins. These differentially expressed proteins had several functions that included energy production and conversion, carbohydrate transport and metabolism, translation, ribosomal structure and biogenesis, posttranslational modification, protein turnover, and chaperone functions. At a systems biology level, the ytfG gene had a synonymous mutation that resulted in significantly downregulated expression at both transcriptomic and proteomic levels. The mutation of the ytfG gene may influence fructose and mannose metabolic processes of K. pneumoniae during space flight, which may be beneficial to the field of space microbiology, providing potential therapeutic strategies to combat or prevent infection in astronauts. Copyright © 2015 IMSS. Published by Elsevier Inc. All rights reserved.

  15. Genomic regions in crop–wild hybrids of lettuce are affected differently in different environments: implications for crop breeding

    PubMed Central

    Hartman, Yorike; Hooftman, Danny A P; Uwimana, Brigitte; van de Wiel, Clemens C M; Smulders, Marinus J M; Visser, Richard G F; van Tienderen, Peter H

    2012-01-01

    Many crops contain domestication genes that are generally considered to lower fitness of crop–wild hybrids in the wild environment. Transgenes placed in close linkage with such genes would be less likely to spread into a wild population. Therefore, for environmental risk assessment of GM crops, it is important to know whether genomic regions with such genes exist, and how they affect fitness. We performed quantitative trait loci (QTL) analyses on fitness(-related) traits in two different field environments employing recombinant inbred lines from a cross between cultivated Lactuca sativa and its wild relative Lactuca serriola. We identified a region on linkage group 5 where the crop allele consistently conferred a selective advantage (increasing fitness to 212% and 214%), whereas on linkage group 7, a region conferred a selective disadvantage (reducing fitness to 26% and 5%), mainly through delaying flowering. The probability for a putative transgene spreading would therefore depend strongly on the insertion location. Comparison of these field results with greenhouse data from a previous study using the same lines showed considerable differences in QTL patterns. This indicates that care should be taken when extrapolating experiments from the greenhouse, and that the impact of domestication genes has to be assessed under field conditions. PMID:23028403

  16. Comparison of the Gene Coding Contents and Other Unusual Features of the GC-Rich and AT-Rich Branch Probosciviruses

    PubMed Central

    Ling, Paul D.; Long, Simon Y.; Zong, Jian-Chao; Heaggans, Sarah Y.; Qin, Xiang

    2016-01-01

    ABSTRACT Nearly 100 cases of lethal acute hemorrhagic disease in young Asian elephants have been reported worldwide. All tested cases contained high levels of elephant endotheliotropic herpesvirus (EEHV) DNA in pathological blood or tissue samples. Seven known major types of EEHVs have been partially characterized and shown to all belong to the novel Proboscivirus genus. However, the recently determined 206-kb EEHV4 genome proved to represent the prototype of a GC-rich branch virus that is very distinct from the previously published 180-kb EEHV1A, EEHV1B, and EEHV5A genomes, which all fall within an alternative AT-rich branch. Although EEHV4 retains the large family of 7xTM and vGPCR-like genes, six are unique to either just one or the other branch. While both branches display a highly enriched distribution of A and T tracts in intergenic domains, they are generally much larger within the GC-rich branch. Both branches retain the vGCNT1 acetylglucosamine transferase and at least one vOX-2 gene, but the two branches differ by 25 genes overall, with the AT-rich branch encoding a fucosyl transferase (vFUT9) plus two or three more vOX2 proteins and an immunoglobulin-like gene family that are all absent from the GC-rich branch. Several envelope glycoproteins retain only 15 to 20% protein identity or less across the two branches. Finally, the two plausible predicted transcriptional regulatory proteins display no homology at all to those in the alpha-, beta-, or gammaherpesvirus subfamilies. These results reinforce our previous proposal that the probosciviruses should be designated a new subfamily of mammalian herpesviruses. IMPORTANCE Multiple species of herpesviruses from three different lineages of the Proboscivirus genus (EEHV1/6, EEHV2/5, and EEHV3/4/7) infect either Asian or African elephants, but the highly lethal hemorrhagic disease is largely confined to Asian elephant calves and is predominantly associated with EEHV1. In the accompanying paper [P. D. Ling et al

  17. Structure and DNA-Binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-Specific DNA Recognition

    SciTech Connect

    Kim, Suhkmann; Zhang, Ziming; Upchurch, Sean; Isern, Nancy G.; Chen, Yuan

    2004-04-16

    2 ARID is a homologous family of DNA-binding domains that occur in DNA binding proteins from a wide variety of species, ranging from yeast to nematodes, insects, mammals and plants. SWI1, a member of the SWI/SNF protein complex that is involved in chromatin remodeling during transcription, contains the ARID motif. The ARID domain of human SWI1 (also known as p270) does not select for a specific DNA sequence from a random sequence pool. The lack of sequence specificity shown by the SWI1 ARID domain stands in contrast to the other characterized ARID domains, which recognize specific AT-rich sequences. We have solved the three-dimensional structure of human SWI1 ARID using solution NMR methods. In addition, we have characterized non-specific DNA-binding by the SWI1 ARID domain. Results from this study indicate that a flexible long internal loop in ARID motif is likely to be important for sequence specific DNA-recognition. The structure of human SWI1 ARID domain also represents a distinct structural subfamily. Studies of ARID indicate that boundary of the DNA binding structural and functional domains can extend beyond the sequence homologous region in a homologous family of proteins. Structural studies of homologous domains such as ARID family of DNA-binding domains should provide information to better predict the boundary of structural and functional domains in structural genomic studies. Key Words: ARID, SWI1, NMR, structural genomics, protein-DNA interaction.

  18. Genome-Environment Interactions That Modulate Aging: Powerful Targets for Drug Discovery

    PubMed Central

    Wuttke, Daniel; Wood, Shona H.; Plank, Michael; Vora, Chintan

    2012-01-01

    Aging is the major biomedical challenge of this century. The percentage of elderly people, and consequently the incidence of age-related diseases such as heart disease, cancer, and neurodegenerative diseases, is projected to increase considerably in the coming decades. Findings from model organisms have revealed that aging is a surprisingly plastic process that can be manipulated by both genetic and environmental factors. Here we review a broad range of findings in model organisms, from environmental to genetic manipulations of aging, with a focus on those with underlying gene-environment interactions with potential for drug discovery and development. One well-studied dietary manipulation of aging is caloric restriction, which consists of restricting the food intake of organisms without triggering malnutrition and has been shown to retard aging in model organisms. Caloric restriction is already being used as a paradigm for developing compounds that mimic its life-extension effects and might therefore have therapeutic value. The potential for further advances in this field is immense; hundreds of genes in several pathways have recently emerged as regulators of aging and caloric restriction in model organisms. Some of these genes, such as IGF1R and FOXO3, have also been associated with human longevity in genetic association studies. The parallel emergence of network approaches offers prospects to develop multitarget drugs and combinatorial therapies. Understanding how the environment modulates aging-related genes may lead to human applications and disease therapies through diet, lifestyle, or pharmacological interventions. Unlocking the capacity to manipulate human aging would result in unprecedented health benefits. PMID:22090473

  19. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus.

    PubMed

    Patel, Chirag J; Chen, Rong; Kodama, Keiichi; Ioannidis, John P A; Butte, Atul J

    2013-05-01

    Diseases such as type 2 diabetes (T2D) result from environmental and genetic factors, and risk varies considerably in the population. T2D-related genetic loci discovered to date explain only a small portion of the T2D heritability. Some heritability may be due to gene-environment interactions. However, documenting these interactions has been difficult due to low availability of concurrent genetic and environmental measures, selection bias, and challenges in controlling for multiple hypothesis testing. Through genome-wide association studies (GWAS), investigators have identified over 90 single nucleotide polymorphisms (SNPs) associated to T2D. Using a method analogous to GWAS [environment-wide association study (EWAS)], we found five environmental factors associated with the disease. By focusing on risk factors that emerge from GWAS and EWAS, it is possible to overcome difficulties in uncovering gene-environment interactions. Using data from the National Health and Nutrition Examination Survey (NHANES), we screened 18 SNPs and 5 serum-based environmental factors for interaction in association to T2D. We controlled for multiple hypotheses using false discovery rate (FDR) and Bonferroni correction and found four interactions with FDR <20 %. The interaction between rs13266634 (SLC30A8) and trans-β-carotene withstood Bonferroni correction (corrected p = 0.006, FDR <1.5 %). The per-risk-allele effect sizes in subjects with low levels of trans-β-carotene were 40 % greater than the marginal effect size [odds ratio (OR) 1.8, 95 % CI 1.3-2.6]. We hypothesize that impaired function driven by rs13266634 increases T2D risk when combined with serum levels of nutrients. Unbiased consideration of environmental and genetic factors may help identify larger and more relevant effect sizes for disease associations.

  20. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.

    PubMed

    Busche, Stephan; Shao, Xiaojian; Caron, Maxime; Kwan, Tony; Allum, Fiona; Cheung, Warren A; Ge, Bing; Westfall, Susan; Simon, Marie-Michelle; Barrett, Amy; Bell, Jordana T; McCarthy, Mark I; Deloukas, Panos; Blanchette, Mathieu; Bourque, Guillaume; Spector, Timothy D; Lathrop, Mark; Pastinen, Tomi; Grundberg, Elin

    2015-12-23

    CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution. Purely invariable CpGs display a bimodal distribution with enrichment of unmethylated CpGs and depletion of fully methylated CpGs in promoter and enhancer regions. Population-variable CpGs account for approximately 15-20 % of total CpGs per tissue, are enriched in enhancer-associated regions and depleted in promoters, and single nucleotide polymorphisms at CpGs are a frequent confounder of extreme methylation variation. Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific. Tobacco smoking is associated with differential methylation in blood with no evidence of this exposure impacting cell counts. Opposite to non-genetic effects, genetic effects of CpG methylation are shared across tissues and thus limit inter-tissue epigenetic drift. CpH methylation is rare, and shows similar characteristics of variation patterns as CpGs. Our study highlights the utility of low pass whole-genome bisulfite sequencing in identifying methylome variation beyond promoter regions, and suggests that targeting the population dynamic methylome of tissues requires assessment of understudied intergenic CpGs distal to gene promoters to reveal the full extent of inter-individual variation.

  1. Draft Genome Sequence of Bacillus cereus LCR12, a Plant Growth–Promoting Rhizobacterium Isolated from a Heavy Metal–Contaminated Environment

    PubMed Central

    Egidi, Eleonora; Wood, Jennifer L.; Mathews, Elizabeth; Fox, Edward; Liu, Wuxing

    2016-01-01

    Bacillus cereus LCR12 is a plant growth–promoting rhizobacterium, isolated from a heavy metal–contaminated environment. The 6.01-Mb annotated genome sequence provides the genetic basis for revealing its potential application to remediate contaminated soils in association with plants. PMID:27688340

  2. The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

    PubMed Central

    Qiao, Qin; Huang, Yanyan; Qi, Ji; Qu, Mingzhi; Jiang, Chen; Lin, Pengcheng; Li, Renhui; Song, Lirong; Yonezawa, Takahiro; Hasegawa, Masami; Crabbe, M. James C.; Chen, Fan; Zhang, Ticao; Zhong, Yang

    2016-01-01

    The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP. PMID:27381465

  3. Draft Genome Sequence of Bacillus cereus LCR12, a Plant Growth-Promoting Rhizobacterium Isolated from a Heavy Metal-Contaminated Environment.

    PubMed

    Egidi, Eleonora; Wood, Jennifer L; Mathews, Elizabeth; Fox, Edward; Liu, Wuxing; Franks, Ashley E

    2016-09-29

    Bacillus cereus LCR12 is a plant growth-promoting rhizobacterium, isolated from a heavy metal-contaminated environment. The 6.01-Mb annotated genome sequence provides the genetic basis for revealing its potential application to remediate contaminated soils in association with plants. Copyright © 2016 Egidi et al.

  4. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Glass, N Louise [UC Berkeley

    2016-07-12

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  5. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Glass, N Louise

    2012-03-22

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  6. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Mosier, Annika [Stanford University

    2016-07-12

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  7. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Mosier, Annika

    2012-03-22

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  8. Comparative community genomics in the Dead Sea: an increasingly extreme environment.

    PubMed

    Bodaker, Idan; Sharon, Itai; Suzuki, Marcelino T; Feingersch, Roi; Shmoish, Michael; Andreishcheva, Ekaterina; Sogin, Mitchell L; Rosenberg, Mira; Maguire, Michael E; Belkin, Shimshon; Oren, Aharon; Béjà, Oded

    2010-03-01

    Owing to the extreme salinity ( approximately 10 times saltier than the oceans), near toxic magnesium levels (approximately 2.0 M Mg(2+)), the dominance of divalent cations, acidic pH (6.0) and high-absorbed radiation flux rates, the Dead Sea represents a unique and harsh ecosystem. Measures of microbial presence (microscopy, pigments and lipids) indicate that during rare bloom events after exceptionally rainy seasons, the microbial communities can reach high densities. However, most of the time, when the Dead Sea level is declining and halite is precipitating from the water column, it is difficult to reliably measure the presence of microorganisms and their activities. Although a number of halophilic Archaea have been previously isolated from the Dead Sea, polar lipid analyses of biomass collected during Dead Sea blooms suggested that these isolates were not the major components of the microbial community of these blooms. In this study, in an effort to characterize the perennial microbial community of the Dead Sea and compare it with bloom assemblages, we performed metagenomic analyses of concentrated biomass from hundreds of liters of brine and of microbial material from the last massive Dead Sea bloom. The difference between the two conditions was reflected in community composition and diversity, in which the bloom was different and less diverse from the residual brine population. The distributional patterns of microbial genes suggested Dead Sea community trends in mono- and divalent cation metabolisms as well as in transposable elements. This may indicate possible mechanisms and pathways enabling these microbes to survive in such a harsh environment.

  9. The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

    PubMed Central

    Lee, Kevin C.; Stott, Matthew B.; Dunfield, Peter F.; Huttenhower, Curtis; McDonald, Ian R.

    2016-01-01

    ABSTRACT Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. IMPORTANCE This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare

  10. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

    PubMed

    Tighe, Scott; Afshinnekoo, Ebrahim; Rock, Tara M; McGrath, Ken; Alexander, Noah; McIntyre, Alexa; Ahsanuddin, Sofia; Bezdan, Daniela; Green, Stefan J; Joye, Samantha; Stewart Johnson, Sarah; Baldwin, Don A; Bivens, Nathan; Ajami, Nadim; Carmical, Joseph R; Herriott, Ian Charold; Colwell, Rita; Donia, Mohamed; Foox, Jonathan; Greenfield, Nick; Hunter, Tim; Hoffman, Jessica; Hyman, Joshua; Jorgensen, Ellen; Krawczyk, Diana; Lee, Jodie; Levy, Shawn; Garcia-Reyero, Natàlia; Settles, Matthew; Thomas, Kelley; Gómez, Felipe; Schriml, Lynn; Kyrpides, Nikos; Zaikova, Elena; Penterman, Jon; Mason, Christopher E

    2017-04-01

    The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.

  11. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP)

    PubMed Central

    Tighe, Scott; Afshinnekoo, Ebrahim; Rock, Tara M.; McGrath, Ken; Alexander, Noah; McIntyre, Alexa; Ahsanuddin, Sofia; Bezdan, Daniela; Green, Stefan J.; Joye, Samantha; Stewart Johnson, Sarah; Baldwin, Don A.; Bivens, Nathan; Ajami, Nadim; Carmical, Joseph R.; Herriott, Ian Charold; Colwell, Rita; Donia, Mohamed; Foox, Jonathan; Greenfield, Nick; Hunter, Tim; Hoffman, Jessica; Hyman, Joshua; Jorgensen, Ellen; Krawczyk, Diana; Lee, Jodie; Levy, Shawn; Garcia-Reyero, Natàlia; Settles, Matthew; Thomas, Kelley; Gómez, Felipe; Schriml, Lynn; Kyrpides, Nikos; Zaikova, Elena; Penterman, Jon; Mason, Christopher E.

    2017-01-01

    The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the “Door to Hell” crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia. PMID:28337070

  12. The Structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA

    SciTech Connect

    Iwahara, Junji; Iwahara, Mizuho; Daughdrill, Gary W.; Ford, Joe J.; Clubb, Robert T.

    2002-03-01

    The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR Spectroscopy, we have determined the first ever three-dimensional structure of an ARID-DNA complex (mol.wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster, ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement. that produces stabilizing contacts from a B-hairpin. Dead ringer's preference for a AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine thymine base step.

  13. Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis[C][W][OPEN

    PubMed Central

    Lowry, David B.; Logan, Tierney L.; Santuari, Luca; Hardtke, Christian S.; Richards, James H.; DeRose-Wilson, Leah J.; McKay, John K.; Sen, Saunak; Juenger, Thomas E.

    2013-01-01

    The regulation of gene expression is crucial for an organism’s development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression. PMID:24045022

  14. From Genes to Environment: Using Integrative Genomics to Build a "Systems-Level" Understanding of Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Hu, Valerie W.

    2013-01-01

    Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders that affect an estimated 1 in 110 individuals. Although there is a strong genetic component associated with these disorders, this review focuses on the multifactorial nature of ASD and how different genome-wide (genomic) approaches contribute to our understanding of autism.…

  15. From Genes to Environment: Using Integrative Genomics to Build a "Systems-Level" Understanding of Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Hu, Valerie W.

    2013-01-01

    Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders that affect an estimated 1 in 110 individuals. Although there is a strong genetic component associated with these disorders, this review focuses on the multifactorial nature of ASD and how different genome-wide (genomic) approaches contribute to our understanding of autism.…

  16. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

    PubMed Central

    Dunn, Barbara; Richter, Chandra; Kvitek, Daniel J.; Pugh, Tom; Sherlock, Gavin

    2012-01-01

    Although the budding yeast Saccharomyces cerevisiae is arguably one of the most well-studied organisms on earth, the genome-wide variation within this species—i.e., its “pan-genome”—has been less explored. We created a multispecies microarray platform containing probes covering the genomes of several Saccharomyces species: S. cerevisiae, including regions not found in the standard laboratory S288c strain, as well as the mitochondrial and 2-μm circle genomes–plus S. paradoxus, S. mikatae, S. kudriavzevii, S. uvarum, S. kluyveri, and S. castellii. We performed array-Comparative Genomic Hybridization (aCGH) on 83 different S. cerevisiae strains collected across a wide range of habitats; of these, 69 were commercial wine strains, while the remaining 14 were from a diverse set of other industrial and natural environments. We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole-genome sequencing on nine of these strains. These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae. PMID:22369888

  17. Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants.

    PubMed

    Bromham, Lindell; Hua, Xia; Lanfear, Robert; Cowman, Peter F

    2015-04-01

    A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast, and nuclear genomes and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynonymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate that drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of divergence between populations, generating higher rates of diversification. These observations link mutation in individuals to population-level processes and to patterns of lineage divergence.

  18. Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts.

    PubMed

    Seo, Young-Su; Lim, Jae Yun; Park, Jungwook; Kim, Sunyoung; Lee, Hyun-Hee; Cheong, Hoon; Kim, Sang-Mok; Moon, Jae Sun; Hwang, Ingyu

    2015-05-06

    In addition to human and animal diseases, bacteria of the genus Burkholderia can cause plant diseases. The representative species of rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B. plantarii, which primarily cause grain rot, sheath rot, and seedling blight, respectively, resulting in severe reductions in rice production. Though Burkholderia rice pathogens cause problems in rice-growing countries, comprehensive studies of these rice-pathogenic species aiming to control Burkholderia-mediated diseases are only in the early stages. We first sequenced the complete genome of B. plantarii ATCC 43733T. Second, we conducted comparative analysis of the newly sequenced B. plantarii ATCC 43733T genome with eleven complete or draft genomes of B. glumae and B. gladioli strains. Furthermore, we compared the genome of three rice Burkholderia pathogens with those of other Burkholderia species such as those found in environmental habitats and those known as animal/human pathogens. These B. glumae, B. gladioli, and B. plantarii strains have unique genes involved in toxoflavin or tropolone toxin production and the clustered regularly interspaced short palindromic repeats (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii ATCC 43733T has many common features with those of B. glumae and B. gladioli, this B. plantarii strain has several unique features, including quorum sensing and CRISPR/CRISPR-associated protein (Cas) systems. The complete genome sequence of B. plantarii ATCC 43733T and publicly available genomes of B. glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome analyses among three rice-pathogenic Burkholderia species responsible for tissue rotting and seedling blight. Our results suggest that B. glumae has evolved rapidly, or has undergone rapid genome rearrangements or deletions, in response to the hosts. It also, clarifies the unique features of rice pathogenic Burkholderia species relative to other

  19. Molecular and cytogenetic characterization of an AT-rich satellite DNA family in Urvillea chacoensis Hunz. (Paullinieae, Sapindaceae).

    PubMed

    Urdampilleta, Juan D; de Souza, Anete Pereira; Schneider, Dilaine R S; Vanzela, André L L; Ferrucci, María S; Martins, Eliana R F

    2009-05-01

    Urvillea chacoensis is a climber with 2n = 22 and some terminal AT-rich heterochromatin blocks that differentiate it from other species of the genus. The AT-rich highly repeated satellite DNA was isolated from U. chacoensis by the digestion of total nuclear DNA with HindIII and XbaI and cloned in Escherichia coli. Satellite DNA structure and chromosomal distribution were investigated. DNA sequencing revealed that the repeat length of satDNA ranges between 721 and 728 bp, the percentage of AT-base pairs was about 72-73% and the studied clones showed an identity of 92.5-95.9%. Although this monomer has a tetranucleosomal size, direct imperfect repetitions of ~180 bp subdividing it in four nucleosomal subregions were observed. The results obtained with FISH indicate that this monomer usually appears distributed in the terminal regions of most chromosomes and is associated to heterochromatin blocks observed after DAPI staining. These observations are discussed in relation to the satellite DNA evolution and compared with other features observed in several plant groups.

  20. Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34melT

    PubMed Central

    Pavan, María Elisa; Pavan, Esteban E.; López, Nancy I.; Levin, Laura

    2015-01-01

    Aeromonas salmonicida subsp. pectinolytica 34melT can be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies of A. salmonicida are known fish pathogens, 34melT belongs to the only subspecies isolated solely from the environment. Genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenic Aeromonas. The most relevant phenotypic characteristics of 34melT are pectin degradation, a distinctive trait of A. salmonicida subsp. pectinolytica, and melanin production. Genes coding for three pectate lyases were detected in a cluster, unique to this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34melT is hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenic Aeromonas strains revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis in Aeromonas occurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34melT to a highly polluted environment, as 13 genomic islands were identified in its genome, some of them containing genes coding for fitness-related traits. Heavy metal resistance genes were also found, along with others associated with oxidative and nitrosative stresses. These characteristics, together with melanin production and the ability to use different substrates, may explain the ability of this microorganism to live in an extremely polluted environment. PMID:26025898

  1. The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments.

    PubMed

    Kelley, Joanna L; Yee, Muh-Ching; Brown, Anthony P; Richardson, Rhea R; Tatarenkov, Andrey; Lee, Clarence C; Harkins, Timothy T; Bustamante, Carlos D; Earley, Ryan L

    2016-08-16

    The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression. Over 400 isogenic lineages currently held in laboratories across the globe show considerable among-lineage variation in physiology, behavior, and life history traits that is maintained under common garden conditions. Temperature mediates the development of primary males and also sex change between hermaphrodites and secondary males, which makes the system ideal for the study of sex determination and sexual plasticity. Mangrove rivulus also exhibit remarkable adaptations to living in extreme environments, and the system has great promise to shed light on the evolution of terrestrial locomotion, aerial respiration, and broad tolerances to hypoxia, salinity, temperature, and environmental pollutants. Genome assembly of the mangrove rivulus allows the study of genes and gene families associated with the traits described above. Here we present a de novo assembled reference genome for the mangrove rivulus, with an approximately 900 Mb genome, including 27,328 annotated, predicted, protein-coding genes. Moreover, we are able to place more than 50% of the assembled genome onto a recently published linkage map. The genome provides an important addition to the linkage map and transcriptomic tools recently developed for this species that together provide critical resources for epigenetic, transcriptomic, and proteomic analyses. Moreover, the genome will serve as the foundation for addressing key questions in behavior, physiology, toxicology, and evolutionary biology.

  2. The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments

    PubMed Central

    Kelley, Joanna L.; Yee, Muh-Ching; Brown, Anthony P.; Richardson, Rhea R.; Tatarenkov, Andrey; Lee, Clarence C.; Harkins, Timothy T.; Bustamante, Carlos D.; Earley, Ryan L.

    2016-01-01

    The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression. Over 400 isogenic lineages currently held in laboratories across the globe show considerable among-lineage variation in physiology, behavior, and life history traits that is maintained under common garden conditions. Temperature mediates the development of primary males and also sex change between hermaphrodites and secondary males, which makes the system ideal for the study of sex determination and sexual plasticity. Mangrove rivulus also exhibit remarkable adaptations to living in extreme environments, and the system has great promise to shed light on the evolution of terrestrial locomotion, aerial respiration, and broad tolerances to hypoxia, salinity, temperature, and environmental pollutants. Genome assembly of the mangrove rivulus allows the study of genes and gene families associated with the traits described above. Here we present a de novo assembled reference genome for the mangrove rivulus, with an approximately 900 Mb genome, including 27,328 annotated, predicted, protein-coding genes. Moreover, we are able to place more than 50% of the assembled genome onto a recently published linkage map. The genome provides an important addition to the linkage map and transcriptomic tools recently developed for this species that together provide critical resources for epigenetic, transcriptomic, and proteomic analyses. Moreover, the genome will serve as the foundation for addressing key questions in behavior, physiology, toxicology, and evolutionary biology. PMID:27324916

  3. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

    PubMed Central

    Sullivan, Matthew B; Huang, Katherine H; Ignacio-Espinoza, Julio C; Berlin, Aaron M; Kelly, Libusha; Weigele, Peter R; DeFrancesco, Alicia S; Kern, Suzanne E; Thompson, Luke R; Young, Sarah; Yandava, Chandri; Fu, Ross; Krastins, Bryan; Chase, Michael; Sarracino, David; Osburne, Marcia S; Henn, Matthew R; Chisholm, Sallie W

    2010-01-01

    T4-like myoviruses are ubiquitous, and their genes are among the most abundant documented in ocean systems. Here we compare 26 T4-like genomes, including 10 from non-cyanobacterial myoviruses, and 16 from marine cyanobacterial myoviruses (cyanophages) isolated on diverse Prochlorococcus or Synechococcus hosts. A core genome of 38 virion construction and DNA replication genes was observed in all 26 genomes, with 32 and 25 additional genes shared among the non-cyanophage and cyanophage subsets, respectively. These hierarchical cores are highly syntenic across the genomes, and sampled to saturation. The 25 cyanophage core genes include six previously described genes with putative functions (psbA, mazG, phoH, hsp20, hli03, cobS), a hypothetical protein with a potential phytanoyl-CoA dioxygenase domain, two virion structural genes, and 16 hypothetical genes. Beyond previously described cyanophage-encoded photosynthesis and phosphate stress genes, we observed core genes that may play a role in nitrogen metabolism during infection through modulation of 2-oxoglutarate. Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements. As well, phages isolated on Synechococcus had higher genome-wide %G+C and often contained different gene subsets (e.g. petE, zwf, gnd, prnA, cpeT) than those isolated on Prochlorococcus. However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection. Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets. PMID:20662890

  4. Genome-Wide Identification of Small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and Their Regulation Role in the Adaption to Gastrointestinal Environment

    PubMed Central

    Zhu, De-Quan; Liu, Fei; Sun, Yu; Yang, Li-Mei; Xin, Li; Meng, Xiang-Chen

    2015-01-01

    Objective Bifidobacteria are one of the predominant bacterial species in the human gastrointestinal tract (GIT) and play a vital role in the host’s health by acting as probiotics. However, how they regulate themselves to adapt to GIT of their host remains unknown. Methods Eighteen bifidobacterial strains were used to analyze their adaptive capacities towards simulated GIT environment. The strain with highest survival rate and adhesion ability was selected for comparative genome as well as transcriptomic analysis. Results The Bifidobacterium animalis subsp. lactis KLDS 2.0603 strain was demonstrated to have the highest survival rate and adhesion ability in simulated GIT treatments. The comparative genome analysis revealed that the KLDS 2.0603 has most similar whole genome sequence compared with BB-12 strain. Eleven intergenic sRNAs were identified after genomes prediction and transcriptomic analysis of KLDS 2.0603. Transcriptomic analysis also showed that genes (mainly sRNAs targeted genes) and sRNAs were differentially expressed in different stress conditions, suggesting that sRNAs might play a crucial role in regulating genes involved in the stress resistance of this strain towards environmental changes. Conclusions This study first provided deep and comprehensive insights into the regulation of KLDS 2.0603 strain at transcription and post-transcription level towards environmental. PMID:25706951

  5. From Genes to Environment: Using integrative genomics to build a “systems level” understanding of autism spectrum disorders

    PubMed Central

    Hu, Valerie W.

    2012-01-01

    Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders that affect an estimated 1 in 110 individuals. Although there is a strong genetic component associated with these disorders, this review focuses on the multi-factorial nature of ASD and how different genome-wide (genomic) approaches contribute to our understanding of autism. Emphasis is placed on the need to study defined ASD phenotypes as well as to integrate large-scale ‘omics’ data in order to develop a “systems level” perspective of ASD which, in turn, is necessary to allow predictions regarding responses to specific perturbations and interventions. PMID:22497667

  6. From genes to environment: using integrative genomics to build a "systems-level" understanding of autism spectrum disorders.

    PubMed

    Hu, Valerie W

    2013-01-01

    Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders that affect an estimated 1 in 110 individuals. Although there is a strong genetic component associated with these disorders, this review focuses on the multifactorial nature of ASD and how different genome-wide (genomic) approaches contribute to our understanding of autism. Emphasis is placed on the need to study defined ASD phenotypes as well as to integrate large-scale "omics" data in order to develop a "systems-level" perspective of ASD, which in turn is necessary to allow predictions regarding responses to specific perturbations and interventions. © 2012 The Author. Child Development © 2012 Society for Research in Child Development, Inc.

  7. Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes.

    PubMed

    Kumar, Sunil; Xue, Liang; Arya, Dev P

    2011-05-18

    A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ∼10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT

  8. Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains

    PubMed Central

    Fagerlund, Annette; Langsrud, Solveig; Schirmer, Bjørn C. T.; Møretrø, Trond; Heir, Even

    2016-01-01

    Listeria monocytogenes is an important foodborne pathogen responsible for the disease listeriosis, and can be found throughout the environment, in many foods and in food processing facilities. The main cause of listeriosis is consumption of food contaminated from sources in food processing environments. Persistence in food processing facilities has previously been shown for the L. monocytogenes sequence type (ST) 8 subtype. In the current study, five ST8 strains were subjected to whole-genome sequencing and compared with five additionally available ST8 genomes, allowing comparison of strains from salmon, poultry and cheese industry, in addition to a human clinical isolate. Genome-wide analysis of single-nucleotide polymorphisms (SNPs) confirmed that almost identical strains were detected in a Danish salmon processing plant in 1996 and in a Norwegian salmon processing plant in 2001 and 2011. Furthermore, we show that L. monocytogenes ST8 was likely to have been transferred between two poultry processing plants as a result of relocation of processing equipment. The SNP data were used to infer the phylogeny of the ST8 strains, separating them into two main genetic groups. Within each group, the plasmid and prophage content was almost entirely conserved, but between groups, these sequences showed strong divergence. The accessory genome of the ST8 strains harbored genetic elements which could be involved in rendering the ST8 strains resilient to incoming mobile genetic elements. These included two restriction-modification loci, one of which was predicted to show phase variable recognition sequence specificity through site-specific domain shuffling. Analysis indicated that the ST8 strains harbor all important known L. monocytogenes virulence factors, and ST8 strains are commonly identified as the causative agents of invasive listeriosis. Therefore, the persistence of this L. monocytogenes subtype in food processing facilities poses a significant concern for food safety

  9. The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment.

    PubMed

    De Luca, Gilles; Barakat, Mohamed; Ortet, Philippe; Fochesato, Sylvain; Jourlin-Castelli, Cécile; Ansaldi, Mireille; Py, Béatrice; Fichant, Gwennaele; Coutinho, Pedro M; Voulhoux, Romé; Bastien, Olivier; Maréchal, Eric; Henrissat, Bernard; Quentin, Yves; Noirot, Philippe; Filloux, Alain; Méjean, Vincent; DuBow, Michael S; Barras, Frédéric; Barbe, Valérie; Weissenbach, Jean; Mihalcescu, Irina; Verméglio, André; Achouak, Wafa; Heulin, Thierry

    2011-01-01

    Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed.

  10. Binding the mammalian high mobility group protein AT-hook 2 to AT-rich deoxyoligonucleotides: enthalpy-entropy compensation.

    PubMed

    Joynt, Suzanne; Morillo, Victor; Leng, Fenfei

    2009-05-20

    HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)(2) is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5'-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3' (FL-AT-1) and 5'-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3' (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to approximately 200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar.

  11. Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation

    PubMed Central

    Joynt, Suzanne; Morillo, Victor; Leng, Fenfei

    2009-01-01

    HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)2 is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5′-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3′ (FL-AT-1) and 5′-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3′ (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to ∼200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar. PMID:19450485

  12. The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments

    SciTech Connect

    Aklujkar, Muktak; Young, Nelson D; Holmes, Dawn; Chavan, Milind; Risso, Carla; Kiss, Hajnalka; Han, Cliff; Land, Miriam L; Lovley, Derek

    2010-01-01

    Background. Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. Results. Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. Conclusion. Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in

  13. Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program

    USDA-ARS?s Scientific Manuscript database

    Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, in using datasets that are unbalanced over time and space, there is increasing exposure to particular genoty...

  14. Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits Robust Nutrient Metabolism in Harsh Environments

    PubMed Central

    Wang, Yang; He, Kaiyong; Jiang, Yongzhong; Shen, Jiate

    2016-01-01

    Pontibacter akesuensis strain AKS 1T was found in Akesu, Xinjiang Province, China, and exhibits the extraordinary ability to metabolize various substrates and is resistant to solar radiation. To gain insight into the bacterial genetic determinants for this adaptability, we report the complete genome sequence of strain AKS 1T. PMID:27795233

  15. Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment

    PubMed Central

    2013-01-01

    investigation of the unclear association of dairy and clinical Sii with human diseases. Conclusions The genome of the African dairy isolate Sii CJ18 clearly differs from the human isolate ATCC BAA-102T. CJ18 possesses a high natural competence predisposition likely explaining the enlarged genome. Metabolic adaptations to the dairy environment are evident and especially lactose uptake corresponds to S. thermophilus. Genome decay is not as advanced as in S. thermophilus (10-19%) possibly due to a shorter history in dairy fermentations. PMID:23521820

  16. Genome Wide Gene by Environment Interaction Analysis Identifies Common SNPs at 17q21.2 that Are Associated with Increased Body Mass Index Only among Asthmatics

    DTIC Science & Technology

    2015-12-16

    Identifies Common SNPs at 17q21.2 that Are Associated with Increased Body Mass Index Only among Asthmatics 5a. CONTRACT NUMBER 5b. GRANT...that are associated with asthma-related BMI increase, we performed a genome-wide gene by environment (asthma) interaction analysis for the outcome of...Seven SNPs clustered in 17q21.2 were identified to be associated with higher BMI among asthmatics (interaction p < 5×10-7 in MESA and p < 0.05 in

  17. Antarctic Genomics

    PubMed Central

    Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

  18. Special AT-rich sequence-binding protein 1: a novel biomarker predicting cervical squamous cell carcinoma prognosis and lymph node metastasis.

    PubMed

    Wang, Shuxiang; Wang, Le; Zhang, Yu; Liu, Yunduo; Meng, Fanling; Ma, Jingquan; Shang, Pan; Gao, Ya; Huang, Qi; Chen, Xiuwei

    2015-09-01

    Special AT-rich sequence-binding protein 1 is aberrantly expressed in various malignant tumors. However, the expression and function of special AT-rich sequence-binding protein 1 in cervical squamous cell carcinoma have not been reported. The objective of this study was to investigate the clinical significance of special AT-rich sequence-binding protein 1 in cervical squamous cell carcinoma. In this study, we investigated the expression of special AT-rich sequence-binding protein 1 through immunohistochemistry in 25 normal cervix specimens and 167 cervical squamous cell carcinomas and analyzed its association with various clinicopathologic parameters, including patient outcome. Special AT-rich sequence-binding protein 1 protein was detected in 58 (34.7%) out of 167 patients and was highly related to International Federation of Gynecology and Obstetrics stage, histologic grade, lymph node metastasis, vascular-lymphatic invasion and recurrence of cervical squamous cell carcinoma. Patients with positive special AT-rich sequence-binding protein 1 expression had significantly lower overall survival and disease-free survival compared with patients with negative expression of special AT-rich sequence-binding protein 1 (P = 0.001 and P < 0.001, respectively). A multivariate Cox regression analysis revealed that special AT-rich sequence-binding protein 1 was an independent prognostic marker for both disease-free survival and overall survival of cervical squamous cell carcinoma patients (P = 0.038 and P = 0.010, respectively). A multivariate logistic regression analysis showed that special AT-rich sequence-binding protein 1 expression was strongly associated with lymph node metastasis (odds ratio = 2.497; P = 0.032). Sensitivity and specificity of special AT-rich sequence-binding protein 1 for lymph node metastasis were 61.0 and 73.8%, respectively. These results showed that special AT-rich sequence-binding protein 1 expression was associated with tumor progression

  19. Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment

    PubMed Central

    Milani, Christian; Turroni, Francesca; Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Ferrario, Chiara; van Sinderen, Douwe

    2015-01-01

    Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome. PMID:26590291

  20. Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

    PubMed Central

    Kumar, Satish; Molloy, Claire; Muñoz, Patricio; Daetwyler, Hans; Chagné, David; Volz, Richard

    2015-01-01

    The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families. PMID:26497141

  1. Survival in extreme environment by "preserve-expand-specialize" strategy: lessons from comparative genomics of an anhydrobiotic midge.

    NASA Astrophysics Data System (ADS)

    Gusev, Oleg; Sugimoto, Manabu; Novikova, Nataliya; Sychev, Vladimir; Okuda, Takashi; Kikawada, Takahiro

    2012-07-01

    Anhydrobiotic chironomid larvae of Polypedilum vanderplanki (Diptera) can withstand prolonged complete desiccation as well as other external stresses including ionizing radiation. Recent experiments showed that this insect is able to survive long-tern exposure to real outer space. At the same time, we found that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. Analysis of several remote populations of the chironomid in Africa that desiccation-related DNA damage might be a driving genetic force for rapid radiation within the species. First results of ongoing genome project suggest that origin and evolution of anhydrobiosis in this single insect species related to rapid duplication of the genes, coding late embryogenesis abundant proteins (LEA) and other molecular agents directly involved in desiccation resistance in the cells. Analysis of genome-wide mRNA expression profiles in the larvae subjected to desiccation shows that joint-activity of large multiple-genes coding regions in the genome involved in control of anhydrobiosis-related molecular adaptations in the chironomid.

  2. Genotype-environment interactions in microsatellite stable/microsatellite instability-low colorectal cancer: results from a genome-wide association study.

    PubMed

    Figueiredo, Jane C; Lewinger, Juan Pablo; Song, Chi; Campbell, Peter T; Conti, David V; Edlund, Christopher K; Duggan, Dave J; Rangrej, Jagadish; Lemire, Mathieu; Hudson, Thomas; Zanke, Brent; Cotterchio, Michelle; Gallinger, Steven; Jenkins, Mark; Hopper, John; Haile, Robert; Newcomb, Polly; Potter, John; Baron, John A; Le Marchand, Loic; Casey, Graham

    2011-05-01

    Genome-wide association studies (GWAS) have led to the identification of a number of common susceptibility loci for colorectal cancer (CRC); however, none of these GWAS have considered gene-environment (G × E) interactions. Therefore, it is unclear whether current hits are modified by environmental exposures or whether there are additional hits whose effects are dependent on environmental exposures. We conducted a systematic search for G × E interactions using genome wide data from the Colon Cancer Family Registry that included 1,191 cases of microsatellite stable (MSS) or microsatellite instability-low (MSI-L) CRC and 999 controls genotyped using either the Illumina Human1M or Human1M-Duo BeadChip. We tested for interactions between genotypes and 14 environmental factors using 3 methods: a traditional case-control test, a case-only test, and the recently proposed 2-step method by Murcray and colleagues. All potentially significant findings were replicated in the ARCTIC Study. No G × E interactions were identified that reached genome-wide significance by any of the 3 methods. When analyzing previously reported susceptibility loci, 7 significant G × E interactions were found at a 5% significance level. We investigated these 7 interactions in an independent sample and none of the interactions were replicated. Identifying G × E interactions will present challenges in a GWAS setting. Our power calculations illustrate the need for larger sample sizes; however, as CRC is a heterogeneous disease, a tradeoff between increasing sample size and heterogeneity needs to be considered. The results from this first genome-wide analysis of G × E in CRC identify several challenges, which may be addressed by large consortium efforts. ©2011 AACR.

  3. Detection of Epistatic and Gene-Environment Interactions Underlying Three Quality Traits in Rice Using High-Throughput Genome-Wide Data.

    PubMed

    Xu, Haiming; Jiang, Beibei; Cao, Yujie; Zhang, Yingxin; Zhan, Xiaodeng; Shen, Xihong; Cheng, Shihua; Lou, Xiangyang; Cao, Liyong

    2015-01-01

    With development of sequencing technology, dense single nucleotide polymorphisms (SNPs) have been available, enabling uncovering genetic architecture of complex traits by genome-wide association study (GWAS). However, the current GWAS strategy usually ignores epistatic and gene-environment interactions due to absence of appropriate methodology and heavy computational burden. This study proposed a new GWAS strategy by combining the graphics processing unit- (GPU-) based generalized multifactor dimensionality reduction (GMDR) algorithm with mixed linear model approach. The reliability and efficiency of the analytical methods were verified through Monte Carlo simulations, suggesting that a population size of nearly 150 recombinant inbred lines (RILs) had a reasonable resolution for the scenarios considered. Further, a GWAS was conducted with the above two-step strategy to investigate the additive, epistatic, and gene-environment associations between 701,867 SNPs and three important quality traits, gelatinization temperature, amylose content, and gel consistency, in a RIL population with 138 individuals derived from super-hybrid rice Xieyou9308 in two environments. Four significant SNPs were identified with additive, epistatic, and gene-environment interaction effects. Our study showed that the mixed linear model approach combining with the GPU-based GMDR algorithm is a feasible strategy for implementing GWAS to uncover genetic architecture of crop complex traits.

  4. Detection of Epistatic and Gene-Environment Interactions Underlying Three Quality Traits in Rice Using High-Throughput Genome-Wide Data

    PubMed Central

    Xu, Haiming; Jiang, Beibei; Cao, Yujie; Zhang, Yingxin; Zhan, Xiaodeng; Shen, Xihong; Cheng, Shihua; Lou, Xiangyang; Cao, Liyong

    2015-01-01

    With development of sequencing technology, dense single nucleotide polymorphisms (SNPs) have been available, enabling uncovering genetic architecture of complex traits by genome-wide association study (GWAS). However, the current GWAS strategy usually ignores epistatic and gene-environment interactions due to absence of appropriate methodology and heavy computational burden. This study proposed a new GWAS strategy by combining the graphics processing unit- (GPU-) based generalized multifactor dimensionality reduction (GMDR) algorithm with mixed linear model approach. The reliability and efficiency of the analytical methods were verified through Monte Carlo simulations, suggesting that a population size of nearly 150 recombinant inbred lines (RILs) had a reasonable resolution for the scenarios considered. Further, a GWAS was conducted with the above two-step strategy to investigate the additive, epistatic, and gene-environment associations between 701,867 SNPs and three important quality traits, gelatinization temperature, amylose content, and gel consistency, in a RIL population with 138 individuals derived from super-hybrid rice Xieyou9308 in two environments. Four significant SNPs were identified with additive, epistatic, and gene-environment interaction effects. Our study showed that the mixed linear model approach combining with the GPU-based GMDR algorithm is a feasible strategy for implementing GWAS to uncover genetic architecture of crop complex traits. PMID:26345334

  5. Assessing causal relationships in genomics: From Bradford-Hill criteria to complex gene-environment interactions and directed acyclic graphs

    PubMed Central

    2011-01-01

    Observational studies of human health and disease (basic, clinical and epidemiological) are vulnerable to methodological problems -such as selection bias and confounding- that make causal inferences problematic. Gene-disease associations are no exception, as they are commonly investigated using observational designs. A rich body of knowledge exists in medicine and epidemiology on the assessment of causal relationships involving personal and environmental causes of disease; it includes seminal causal criteria developed by Austin Bradford Hill and more recently applied directed acyclic graphs (DAGs). However, such knowledge has seldom been applied to assess causal relationships in clinical genetics and genomics, even in studies aimed at making inferences relevant for human health. Conversely, incorporating genetic causal knowledge into clinical and epidemiological causal reasoning is still a largely unexplored area. As the contribution of genetics to the understanding of disease aetiology becomes more important, causal assessment of genetic and genomic evidence becomes fundamental. The method we develop in this paper provides a simple and rigorous first step towards this goal. The present paper is an example of integrative research, i.e., research that integrates knowledge, data, methods, techniques, and reasoning from multiple disciplines, approaches and levels of analysis to generate knowledge that no discipline alone may achieve. PMID:21658235

  6. The host genomic environment of the provirus determines the abundance of HTLV-1–infected T-cell clones

    PubMed Central

    Malani, Nirav; Melamed, Anat; Gormley, Niall; Carter, Richard; Bentley, David; Berry, Charles; Bushman, Frederic D.; Taylor, Graham P.

    2011-01-01

    Human T-lymphotropic virus type 1 (HTLV-1) persists by driving clonal proliferation of infected T lymphocytes. A high proviral load predisposes to HTLV-1–associated diseases. Yet the reasons for the variation within and between persons in the abundance of HTLV-1–infected clones remain unknown. We devised a high-throughput protocol to map the genomic location and quantify the abundance of > 91 000 unique insertion sites of the provirus from 61 HTLV-1+ persons and > 2100 sites from in vitro infection. We show that a typical HTLV-1–infected host carries between 500 and 5000 unique insertion sites. We demonstrate that negative selection dominates during chronic infection, favoring establishment of proviruses integrated in transcriptionally silenced DNA: this selection is significantly stronger in asymptomatic carriers. We define a parameter, the oligoclonality index, to quantify clonality. The high proviral load characteristic of HTLV-1–associated inflammatory disease results from a larger number of unique insertion sites than in asymptomatic carriers and not, as previously thought, from a difference in clonality. The abundance of established HTLV-1 clones is determined by genomic features of the host DNA flanking the provirus. HTLV-1 clonal expansion in vivo is favored by orientation of the provirus in the same sense as the nearest host gene. PMID:21228324

  7. Special AT-rich Binding Protein-2 (SATB2) Differentially Affects Disease-causing p63 Mutant Proteins*

    PubMed Central

    Chung, Jacky; Grant, R. Ian; Kaplan, David R.; Irwin, Meredith S.

    2011-01-01

    p63, a p53 family member, is critical for proper skin and limb development and directly regulates gene expression in the ectoderm. Mice lacking p63 exhibit skin and craniofacial defects including cleft palate. In humans p63 mutations are associated with several distinct developmental syndromes. p63 sterile-α-motif domain, AEC (ankyloblepharon-ectodermal dysplasia-clefting)-associated mutations are associated with a high prevalence of orofacial clefting disorders, which are less common in EEC (ectrodactyly-ectodermal dysplasia-clefting) patients with DNA binding domain p63 mutations. However, the mechanisms by which these mutations differentially influence p63 function remain unclear, and interactions with other proteins implicated in craniofacial development have not been identified. Here, we show that AEC p63 mutations affect the ability of the p63 protein to interact with special AT-rich binding protein-2 (SATB2), which has recently also been implicated in the development of cleft palate. p63 and SATB2 are co-expressed early in development in the ectoderm of the first and second branchial arches, two essential sites where signaling is required for craniofacial patterning. SATB2 attenuates p63-mediated gene expression of perp (p53 apoptosis effector related to PMP-22), a critical downstream target gene during development, and specifically decreases p63 perp promoter binding. Interestingly, AEC but not EEC p63 mutations affect the ability of p63 to interact with SATB2 and the inhibitory effects of SATB2 on p63 transactivation of perp are most pronounced for AEC-associated p63 mutations. Our findings reveal a novel gain-of-function property of AEC-causing p63 mutations and identify SATB2 as the first p63 binding partner that differentially influences AEC and EEC p63 mutant proteins. PMID:21965674

  8. Disease activity in systemic lupus erythematosus correlates with expression of the transcription factor AT-rich-interactive domain 3A.

    PubMed

    Ward, Julie M; Rose, Kira; Montgomery, Courtney; Adrianto, Indra; James, Judith A; Merrill, Joan T; Webb, Carol F

    2014-12-01

    Systemic lupus erythematosus (SLE) is a complex and multifactorial autoimmune disease with striking clinical, immunologic, and genetic heterogeneity, despite nearly ubiquitous antinuclear antibody (ANA) production. Multiple gene polymorphisms have been associated with the disease, but these individually account for only a very small percentage of overall SLE risk. In earlier studies, constitutive expression of the DNA-binding protein AT-rich-interactive domain 3A (ARID3a) in transgenic mouse B lymphocyte lineage cells led to spontaneous ANA production and preferential development of B cells associated with production of polyreactive antibodies. Therefore, we undertook this study to determine whether ARID3a was overexpressed in B lymphocytes of SLE patients and whether ARID3a expression was associated with disease severity. A cross-section of SLE patients, rheumatoid arthritis patients, and age- and sex-matched controls was analyzed longitudinally for lupus disease activity, numbers of ARID3a+ peripheral blood mononuclear B cells from multiple B cell subsets, and immunoglobulin and cytokine levels. Fifty of 115 SLE patients (43%) had dramatically increased numbers of ARID3a+ B cells compared to healthy controls. ARID3a was not expressed in naive B cells of healthy controls, but was abundant in these precursors of antibody-secreting cells in SLE patients. Total numbers of ARID3a+ B cells correlated with increased disease activity as defined by SLE Disease Activity Index scores in individuals assessed at 3 time points. These findings identify B cell anomalies in SLE that allow stratification of patient samples based on ARID3a expression and implicate ARID3a as a potential marker of CD19+ B lymphocytes correlated with disease activity. Copyright © 2014 by the American College of Rheumatology.

  9. A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica.

    PubMed

    Krishnan, Neeraja M; Pattnaik, Swetansu; Jain, Prachi; Gaur, Prakhar; Choudhary, Rakshit; Vaidyanathan, Srividya; Deepak, Sa; Hariharan, Arun K; Krishna, Pg Bharath; Nair, Jayalakshmi; Varghese, Linu; Valivarthi, Naveen K; Dhas, Kunal; Ramaswamy, Krishna; Panda, Binay

    2012-09-09

    The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach. The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.

  10. Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: the amazing dinoflagellates.

    PubMed

    Moreno Díaz de la Espina, Susana; Alverca, Elsa; Cuadrado, Angeles; Franca, Susana

    2005-03-01

    Dinoflagellates are fascinating protists that have attracted researchers from different fields. The free-living species are major primary producers and the cause of harmful algal blooms sometimes associated with red tides. Dinoflagellates lack histones and nucleosomes and present a unique genome and chromosome organization, being considered the only living knockouts of histones. Their plastids contain genes organized in unigenic minicircles. Basic cell structure, biochemistry and molecular phylogeny place the dinoflagellates firmly among the eukaryotes. They have G1-S-G2-M cell cycles, repetitive sequences, ribosomal genes in tandem, nuclear matrix, snRNAs, and eukaryotic cytoplasm, whereas their nuclear DNA is different, from base composition to chromosome organization. They have a high G + C content, highly methylated and rare bases such as 5-hydroxymethyluracil (HOMeU), no TATA boxes, and form distinct interphasic dinochromosomes with a liquid crystalline organization of DNA, stabilized by metal cations and structural RNA. Without histones and with a protein:DNA mass ratio (1:10) lower than prokaryotes, they need a different way of packing their huge amounts of DNA into a functional chromatin. In spite of the high interest in the dinoflagellate system in genetics, molecular and cellular biology, their analysis until now has been very restricted. We review here the main achievements in the characterization of the genome, nucleus and chromosomes in this diversified phylum. The recent discovery of a eukaryotic structural and functional differentiation in the dinochromosomes and of the organization of gene expression in them, demonstrate that in spite of the secondary loss of histones, that produce a lack of nucleosomal and supranucleosomal chromatin organization, they keep a functional nuclear organization closer to eukaryotes than to prokaryotes.

  11. Discovering pure gene-environment interactions in blood pressure genome-wide association studies data: a two-step approach incorporating new statistics.

    PubMed

    Wang, Maggie Haitian; Huang, Chien-Hsun; Zheng, Tian; Lo, Shaw-Hwa; Hu, Inchi

    2014-01-01

    Environment has long been known to play an important part in disease etiology. However, not many genome-wide association studies take environmental factors into consideration. There is also a need for new methods to identify the gene-environment interactions. In this study, we propose a 2-step approach incorporating an influence measure that capturespure gene-environment effect. We found that pure gene-age interaction has a stronger association than considering the genetic effect alone for systolic blood pressure, measured by counting the number of single-nucleotide polymorphisms (SNPs)reaching a certain significance level. We analyzed the subjects by dividing them into two age groups and found no overlap in the top identified SNPs between them. This suggested that age might have a nonlinear effect on genetic association. Furthermore, the scores of the top SNPs for the two age subgroups were about 3times those obtained when using all subjects for systolic blood pressure. In addition, the scores of the older age subgroup were much higher than those for the younger group. The results suggest that genetic effects are stronger in older age and that genetic association studies should take environmental effects into consideration, especially age.

  12. Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs.

    PubMed

    Zhang, X; Pérez-Rodríguez, P; Semagn, K; Beyene, Y; Babu, R; López-Cruz, M A; San Vicente, F; Olsen, M; Buckler, E; Jannink, J-L; Prasanna, B M; Crossa, J

    2015-03-01

    One of the most important applications of genomic selection in maize breeding is to predict and identify the best untested lines from biparental populations, when the training and validation sets are derived from the same cross. Nineteen tropical maize biparental populations evaluated in multienvironment trials were used in this study to assess prediction accuracy of different quantitative traits using low-density (~200 markers) and genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs), respectively. An extension of the Genomic Best Linear Unbiased Predictor that incorporates genotype × environment (GE) interaction was used to predict genotypic values; cross-validation methods were applied to quantify prediction accuracy. Our results showed that: (1) low-density SNPs (~200 markers) were largely sufficient to get good prediction in biparental maize populations for simple traits with moderate-to-high heritability, but GBS outperformed low-density SNPs for complex traits and simple traits evaluated under stress conditions with low-to-moderate heritability; (2) heritability and genetic architecture of target traits affected prediction performance, prediction accuracy of complex traits (grain yield) were consistently lower than those of simple traits (anthesis date and plant height) and prediction accuracy under stress conditions was consistently lower and more variable than under well-watered conditions for all the target traits because of their poor heritability under stress conditions; and (3) the prediction accuracy of GE models was found to be superior to that of non-GE models for complex traits and marginal for simple traits.

  13. Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs

    PubMed Central

    Zhang, X; Pérez-Rodríguez, P; Semagn, K; Beyene, Y; Babu, R; López-Cruz, M A; San Vicente, F; Olsen, M; Buckler, E; Jannink, J-L; Prasanna, B M; Crossa, J

    2015-01-01

    One of the most important applications of genomic selection in maize breeding is to predict and identify the best untested lines from biparental populations, when the training and validation sets are derived from the same cross. Nineteen tropical maize biparental populations evaluated in multienvironment trials were used in this study to assess prediction accuracy of different quantitative traits using low-density (~200 markers) and genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs), respectively. An extension of the Genomic Best Linear Unbiased Predictor that incorporates genotype × environment (GE) interaction was used to predict genotypic values; cross-validation methods were applied to quantify prediction accuracy. Our results showed that: (1) low-density SNPs (~200 markers) were largely sufficient to get good prediction in biparental maize populations for simple traits with moderate-to-high heritability, but GBS outperformed low-density SNPs for complex traits and simple traits evaluated under stress conditions with low-to-moderate heritability; (2) heritability and genetic architecture of target traits affected prediction performance, prediction accuracy of complex traits (grain yield) were consistently lower than those of simple traits (anthesis date and plant height) and prediction accuracy under stress conditions was consistently lower and more variable than under well-watered conditions for all the target traits because of their poor heritability under stress conditions; and (3) the prediction accuracy of GE models was found to be superior to that of non-GE models for complex traits and marginal for simple traits. PMID:25407079

  14. Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

    PubMed

    Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

    2014-06-01

    The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

  15. A novel AT-rich DNA binding protein that combines an HMG I-like DNA binding domain with a putative transcription domain.

    PubMed Central

    Tjaden, G; Coruzzi, G M

    1994-01-01

    There is growing evidence that AT-rich promoter elements play a role in transcription of plant genes. For the promoter of the nuclear gene for chloroplast glutamine synthetase from pea (GS2), the deletion of a 33-bp AT-rich sequence (box 1 native) from the 5' end of a GS2 promoter-beta-glucuronidase (GUS) fusion resulted in a 10-fold reduction in GUS activity. The box 1 native element was used in gel shift analysis and two distinct complexes were detected. One complex is related to the low-mobility complex reported previously for AT-rich elements from several other plant promoters. A multimer of the box 1 sequence was used to isolate a cDNA encoding an AT-rich DNA binding protein (ATBP-1). ATBP-1 is not a high-mobility group protein, but it is a novel protein that combines a high-mobility group I/Y-like DNA binding domain with a glutamine-rich putative transcriptional domain. PMID:7907505

  16. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  17. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  18. Genomic Potential of Stenotrophomonas maltophilia in Bioremediation with an Assessment of Its Multifaceted Role in Our Environment

    PubMed Central

    Mukherjee, Piyali; Roy, Pranab

    2016-01-01

    The gram negative bacterium Stenotrophomonas is rapidly evolving as a nosocomial pathogen in immuno-compromised patients. Treatment of Stenotrophomonas maltophilia infections is problematic because of their increasing resistance to multiple antibiotics. This article aims to review the multi-disciplinary role of Stenotrophomonas in our environment with special focus on their metabolic and genetic potential in relation to bioremediation and phytoremediation. Current and emerging treatments and diagnosis for patients infected with S. maltophilia are discussed besides their capability of production of novel bioactive compounds. The plant growth promoting characteristics of this bacterium has been considered with special reference to secondary metabolite production. Nano-particle synthesis by Stenotrophomonas has also been reviewed in addition to their applications as effective biocontrol agents in plant and animal pathogenesis. PMID:27446008

  19. Listeria Genomics

    NASA Astrophysics Data System (ADS)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  20. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes

    PubMed Central

    Ribeiro, Teresa; Barrela, Ricardo M.; Bergès, Hélène; Marques, Cristina; Loureiro, João; Morais-Cecílio, Leonor; Paiva, Jorge A. P.

    2016-01-01

    The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus. PMID:27148332

  1. Genome-wide association analysis to identify genotype × environment interaction for milk protein yield and level of somatic cell score as environmental descriptors in German Holsteins.

    PubMed

    Streit, M; Reinhardt, F; Thaller, G; Bennewitz, J

    2013-01-01

    Genotype by environment interaction (G × E) has been widely reported in dairy cattle. If the environment can be measured on a continuous scale, reaction norms can be applied to study G × E. The average herd milk production level has frequently been used as an environmental descriptor because it is influenced by the level of feeding or the feeding regimen. Another important environmental factor is the level of udder health and hygiene, for which the average herd somatic cell count might be a descriptor. In the present study, we conducted a genome-wide association analysis to identify single nucleotide polymorphisms (SNP) that affect intercept and slope of milk protein yield reaction norms when using the average herd test-day solution for somatic cell score as an environmental descriptor. Sire estimates for intercept and slope of the reaction norms were calculated from around 12 million daughter records, using linear reaction norm models. Sires were genotyped for ~54,000 SNP. The sire estimates were used as observations in the association analysis, using 1,797 sires. Significant SNP were confirmed in an independent validation set consisting of 500 sires. A known major gene affecting protein yield was included as a covariable in the statistical model. Sixty (21) SNP were confirmed for intercept with P ≤ 0.01 (P ≤ 0.001) in the validation set, and 28 and 11 SNP, respectively, were confirmed for slope. Most but not all SNP affecting slope also affected intercept. Comparison with an earlier study revealed that SNP affecting slope were, in general, also significant for slope when the environment was modeled by the average herd milk production level, although the two environmental descriptors were poorly correlated. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  2. Jarid2 (Jumonji, AT rich interactive domain 2) regulates NOTCH1 expression via histone modification in the developing heart.

    PubMed

    Mysliwiec, Matthew R; Carlson, Clayton D; Tietjen, Josh; Hung, Holly; Ansari, Aseem Z; Lee, Youngsook

    2012-01-06

    Jarid2/Jumonji, the founding member of the Jmj factor family, critically regulates various developmental processes, including cardiovascular development. The Jmj family was identified as histone demethylases, indicating epigenetic regulation by Jmj proteins. Deletion of Jarid2 in mice resulted in cardiac malformation and increased endocardial Notch1 expression during development. Although Jarid2 has been shown to occupy the Notch1 locus in the developing heart, the precise molecular role of Jarid2 remains unknown. Here we show that deletion of Jarid2 results in reduced methylation of lysine 9 on histone H3 (H3K9) at the Notch1 genomic locus in embryonic hearts. Interestingly, SETDB1, a histone H3K9 methyltransferase, was identified as a putative cofactor of Jarid2 by yeast two-hybrid screening, and the physical interaction between Jarid2 and SETDB1 was confirmed by coimmunoprecipitation experiments. Concurrently, accumulation of SETDB1 at the site of Jarid2 occupancy was significantly reduced in Jarid2 knock out (KO) hearts. Employing genome-wide approaches, putative Jarid2 target genes regulated by SETDB1 via H3K9 methylation were identified in the developing heart by ChIP-chip. These targets are involved in biological processes that, when dysregulated, could manifest in the phenotypic defects observed in Jarid2 KO mice. Our data demonstrate that Jarid2 functions as a transcriptional repressor of target genes, including Notch1, through a novel process involving the modification of H3K9 methylation via specific interaction with SETDB1 during heart development. Therefore, our study provides new mechanistic insights into epigenetic regulation by Jarid2, which will enhance our understanding of the molecular basis of other organ development and biological processes.

  3. Carbonic anhydrase distribution across organisms and environments: genomic predictors for soil enzymatic fluxes of carbon cycle tracers δ18O and COS

    NASA Astrophysics Data System (ADS)

    Meredith, L. K.; Singer, E.

    2016-12-01

    Carbonyl sulfide (COS) and the oxygen isotope composition (δ18O) of CO2 are potential tools for differentiating the contributions of photosynthesis and respiration to the balance of global carbon cycling. These processes are coupled at the leaf level via the enzyme carbonic anhydrase (CA), which hydrolyzes CO2 in the first biochemical step of the photosynthetic pathway (CO2 + H2O ⇌ HCO3- + H+) and correspondingly structural analogue COS (COS + H2O → CO2 + H2S). CA also accelerates the exchange of oxygen isotopes between CO2 and H2O leading to a distinct isotopic imprint. The biogeochemical cycles of these tracers include significant, yet poorly characterized soil processes that challenge their utility for probing the carbon cycle. In soils, microbial CA also hydrolyze COS and accelerate O isotope exchange between CO2 and soil water. Genomic predictors of microbial CA activity may help account and predict for these soil fluxes. Using a bioinformatics approach, we assess the distribution of the six known CA classes (α, β, γ, δ, η, ζ) in organisms ranging from fungi and plants to archaea and bacteria, and ask whether CA diversity is linked to soil microbial diversity. We survey the diversity and relative abundance of CA in a wide variety of environments and estimate the sensitivity of CA to biome and land use. Finally, we compare the CA distribution in soils to measurements (oxygen isotope and COS fluxes) and models of CA activity to develop genomic predictors for CA activity. This work provides the first survey of CA in soils, a step towards understanding the significant role of CA in microbial ecology and microbe-mediated biogeochemical cycles.

  4. Characterization of Equine Infectious Anemia Virus Integration in the Horse Genome.

    PubMed

    Liu, Qiang; Wang, Xue-Feng; Ma, Jian; He, Xi-Jun; Wang, Xiao-Jun; Zhou, Jian-Hua

    2015-06-19

    Human immunodeficiency virus (HIV)-1 has a unique integration profile in the human genome relative to murine and avian retroviruses. Equine infectious anemia virus (EIAV) is another well-studied lentivirus that can also be used as a promising retro-transfection vector, but its integration into its native host has not been characterized. In this study, we mapped 477 integration sites of the EIAV strain EIAVFDDV13 in fetal equine dermal (FED) cells during in vitro infection. Published integration sites of EIAV and HIV-1 in the human genome were also analyzed as references. Our results demonstrated that EIAVFDDV13 tended to integrate into genes and AT-rich regions, and it avoided integrating into transcription start sites (TSS), which is consistent with EIAV and HIV-1 integration in the human genome. Notably, the integration of EIAVFDDV13 favored long interspersed elements (LINEs) and DNA transposons in the horse genome, whereas the integration of HIV-1 favored short interspersed elements (SINEs) in the human genome. The chromosomal environment near LINEs or DNA transposons potentially influences viral transcription and may be related to the unique EIAV latency states in equids. The data on EIAV integration in its natural host will facilitate studies on lentiviral infection and lentivirus-based therapeutic vectors.

  5. Genomic variation in the MMP-1 promoter influences estrogen receptor mediated activity in a mechanically activated environment: potential implications for microgravity risk assessment

    NASA Astrophysics Data System (ADS)

    Thaler, John; Myers, Ken; Lu, Ting; Hart, David

    examine the potential impact of the 1G/2G SNP on the cellular response to mechanical loading. HIG-82 cells are estrogen receptor (ER) negative and were transiently transfected with SV40 expression vectors for either ER-α or ER-β isoforms. Cells grown on glass slides were also co-transfected with either a 1G or 2G MMP-1 promoter-luciferase construct. Transfected cells were subjected to dynamic shear stress in a Flexcell Streamer Shear Stress Device. The dynamic loading regime was 0.5 Hz, 10 dyn/cm2 shear for 1 minute followed by 14 minutes rest and repeated for 8 hrs. A Promega Dual Luciferase Reporter Assay System was used to assess MMP-1 promoter activity. Results: Shear stress loading increased both 1G and 2G MMP-1 promoter activity compared to unloaded controls, however the 2G promoter had significantly higher rates of expression than the 1G promoter across all loading regimes and ER co-transfections. Transfection with ER-β resulted in higher MMP-1 promoter activity than that in cells expressing ER-α or in ER-neg cells. Conclusions: Specific genomic variations can lead to differences in cellular responses to changes in mechanical loading environments such as are encountered in microgravity environments or earth-based analogs. These genomic differences may predispose individuals to greater risk of bone loss. It is important to understand the combined effects of mechanical loading, genetic variation and sex hormones on bone maintenance so that risks can be identified for microgravity or analog environments, and specific interventions developed to counteract such risk or even exclude some individuals from prolonged space environments due to the extent of the risk.

  6. Genetic environment of the KPC gene in Acinetobacter baumannii ST2 clone from Puerto Rico and genomic insights into its drug resistance.

    PubMed

    Martinez, Teresa; Martinez, Idali; Vazquez, Guillermo J; Aquino, Edna E; Robledo, Iraida E

    2016-08-01

    Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The Klebsiella pneumoniae carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in Enterobacteriaceae and Pseudomonas aeruginosa isolates associated with transposon Tn4401 commonly located in plasmids. Acinetobacter baumannii has become an important multidrug-resistant nosocomial pathogen. KPC-producing A. baumannii has been reported to date only in Puerto Rico. The objective of this study was to determine the whole genomic sequence of a KPC-producing A. baumannii in order to (i) define its allelic diversity, (ii) identify the location and genetic environment of the blaKPC and (iii) detect additional mechanisms of antimicrobial resistance. Next-generation sequencing, Southern blot, PFGE, multilocus sequence typing and bioinformatics analysis were performed. The organism was assigned to the international ST2 clone. The blaKPC-2 was identified on a novel truncated version of Tn4401e (tentatively named Tn4401h), located in the chromosome within an IncA/C plasmid fragment derived from an Enterobacteriaceae, probably owing to insertion sequence IS26. A chromosomally located truncated Tn1 transposon harbouring a blaTEM-1 was found in a novel genetic environment within an antimicrobial resistance cluster. Additional resistance mechanisms included efflux pumps, non-β-lactam antibiotic inactivating enzymes within and outside a resistance island, two class 1 integrons, In439 and the novel In1252, as well as mutations in the topoisomerase and DNA gyrase genes which confer resistance to quinolones. The presence of the blaKPC in an already globally disseminated A. baumannii ST2 presents a serious threat of further dissemination.

  7. Effect of Introns and AT-Rich Sequences on Expression of the Bacterial Hygromycin B Resistance Gene in the Basidiomycete Schizophyllum commune

    PubMed Central

    Scholtmeijer, Karin; Wösten, Han A. B.; Springer, Jan; Wessels, Joseph G. H.

    2001-01-01

    Previously, it was shown that introns are required for efficient mRNA accumulation in Schizophyllum commune and that the presence of AT-rich sequences in the coding region of genes can result in truncation of transcripts in this homobasidiomycete. Here we show that intron-dependent mRNA accumulation and truncation of transcripts are two independent events that both affect expression of the bacterial hygromycin B resistance gene in S. commune. PMID:11133486

  8. Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation

    PubMed Central

    Hernandez-Romano, Jesus; Carlos-Rivera, Francisco J; Salgado, Heladia; Lamadrid-Figueroa, Hector; Valverde-Garduño, Veronica; Rodriguez, Mario H; Martinez-Barnetche, Jesus

    2008-01-01

    Background Understanding the transcriptional regulation mechanisms in response to environmental challenges is of fundamental importance in biology. Transcription factors associated to response elements and the chromatin structure had proven to play important roles in gene expression regulation. We have analyzed promoter regions of dipteran genes induced in response to immune challenge, in search for particular sequence patterns involved in their transcriptional regulation. Results 5' upstream regions of D. melanogaster and A. gambiae immunity-induced genes and their corresponding orthologous genes in 11 non-melanogaster drosophilid species and Ae. aegypti share enrichment in AT-rich short motifs. AT-rich motifs are associated with nucleosome formation as predicted by two different algorithms. In A. gambiae and D. melanogaster, many immunity genes 5' upstream sequences also showed NFκB response elements, located within 500 bp from the transcription start site. In A. gambiae, the frequency of ATAA motif near the NFκB response elements was increased, suggesting a functional link between nucleosome formation/remodelling and NFκB regulation of transcription. Conclusion AT-rich motif enrichment in 5' upstream sequences in A. gambiae, Ae. aegypti and the Drosophila genus immunity genes suggests a particular pattern of nucleosome formation/chromatin organization. The co-occurrence of such motifs with the NFκB response elements suggests that these sequence signatures may be functionally involved in transcriptional activation during dipteran immune response. AT-rich motif enrichment in regulatory regions in this group of co-regulated genes could represent an evolutionary constrained signature in dipterans and perhaps other distantly species. PMID:18613977

  9. Evolution of the chloroplast genome.

    PubMed Central

    Howe, Christopher J; Barbrook, Adrian C; Koumandou, V Lila; Nisbet, R Ellen R; Symington, Hamish A; Wightman, Tom F

    2003-01-01

    We discuss the suggestion that differences in the nucleotide composition between plastid and nuclear genomes may provide a selective advantage in the transposition of genes from plastid to nucleus. We show that in the adenine, thymine (AT)-rich genome of Borrelia burgdorferi several genes have an AT-content lower than the average for the genome as a whole. However, genes whose plant homologues have moved from plastid to nucleus are no less AT-rich than genes whose plant homologues have remained in the plastid, indicating that both classes of gene are able to support a high AT-content. We describe the anomalous organization of dinoflagellate plastid genes. These are located on small circles of 2-3 kbp, in contrast to the usual plastid genome organization of a single large circle of 100-200 kbp. Most circles contain a single gene. Some circles contain two genes and some contain none. Dinoflagellate plastids have retained far fewer genes than other plastids. We discuss a similarity between the dinoflagellate minicircles and the bacterial integron system. PMID:12594920

  10. Prokaryotic nucleotide composition is shaped by both phylogeny and the environment.

    PubMed

    Reichenberger, Erin R; Rosen, Gail; Hershberg, Uri; Hershberg, Ruth

    2015-04-09

    The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.

  11. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments.

    PubMed

    Zhang, Qian; Gou, Wenyu; Wang, Xiaotong; Zhang, Yawen; Ma, Jun; Zhang, Hongliang; Zhang, Ying; Zhang, Hao

    2016-02-23

    Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments.

  13. Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments

    PubMed Central

    Zhang, Qian; Gou, Wenyu; Wang, Xiaotong; Zhang, Yawen; Ma, Jun; Zhang, Hongliang; Zhang, Ying; Zhang, Hao

    2016-01-01

    Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments. PMID:26907498

  14. Complete genome sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment

    DOE PAGES

    Hwang, C.; Copeland, A.; Lucas, Susan; ...

    2015-01-22

    We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium’s genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation.

  15. Complete genome sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment

    SciTech Connect

    Hwang, C.; Copeland, A.; Lucas, Susan; Lapidus, Alla; Barry, Kerrie W.; Glavina del Rio, T.; Dalin, Eileen; Tice, Hope; Pitluck, S.; Sims, David R.; Brettin, T.; Bruce, David; Detter, J. C.; Han, Cliff F.; Schmutz, Jeremy; Larimer, F.; Land, M.; Hauser, L.; Kyrpides, Nikos C.; Lykidis, Athanasios; Richardson, P. M.; Beliaev, Alex S.; Sanford, Robert A.; Loeffler, Frank E.; Fields, Matthew W.

    2015-01-22

    We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium’s genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation.

  16. OsARID3, an AT-rich Interaction Domain-containing protein, is required for shoot meristem development in rice.

    PubMed

    Xu, Yan; Zong, Wei; Hou, Xin; Yao, Jialing; Liu, Hongbo; Li, Xianghua; Zhao, Yunde; Xiong, Lizhong

    2015-09-01

    The shoot apical meristem (SAM) produces all of the plant's aerial organs. The SAM is established either during embryogenesis or experimentally in in vitro tissue culture. Although several factors including the Class I KNOTTED1-LIKE HOMEOBOX (KNOXI) proteins, auxin, and cytokinin are known to play essential roles in SAM development, the underlying mechanisms of SAM formation and maintenance are still largely not understood. Herein we demonstrate that OsARID3, a member of the rice (Oryza sativa) AT-rich Interaction Domain (ARID) family, is required for SAM development. Disruption of OsARID3 leads to a defective SAM, early seedling lethality, and impaired capacity of in vitro shoot regeneration. We show that the expression levels of several KNOXI genes and the biosynthetic genes for auxin and cytokinin are significantly altered in the Osarid3 mutant calli. Moreover, we determine that auxin concentrations are increased, whereas cytokinin levels are decreased, in Osarid3 calli. Furthermore, chromatin immunoprecipitation results demonstrate that OsARID3 binds directly to the KNOXI gene OSH71, the auxin biosynthetic genes OsYUC1 and OsYUC6, and the cytokinin biosynthetic genes OsIPT2 and OsIPT7. We also show through electrophoretic mobility shift assays that OsARID3 specifically binds to the AT-rich DNA sequences of the identified target genes. We conclude that OsARID3 is an AT-rich specific DNA-binding protein and that it plays a major role in SAM development in rice. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  17. First Azospirillum genome from aquatic environments: Whole-genome sequence of Azospirillum thiophilum BV-S(T), a novel diazotroph harboring a capacity of sulfur-chemolithotrophy from a sulfide spring.

    PubMed

    Kwak, Yunyoung; Shin, Jae-Ho

    2016-02-01

    Azospirillum thiophilum BV-S(T), isolated from a sulfide spring, is a novel nitrogen-fixing bacterium harboring sulfur-lithotrophy. In order to identify genetic characteristics with habitat- and metabolic features contrasting to those from terrestrial Azospirillum species, we present here the genome sequence of a novel species A. thiophilum BV-S(T), with a significance of first genome report in the aquatic Azospirillum species. The genome of strain BV-S(T) is comprised of 7.6Mb chromosome with a GC content of 68.2%. This information will contribute to expand understandings of sulfur-oxidizer microbes that preserve inherencies as a diazotroph, and further it will provide insights into genome plasticity of the genus Azospirillum for niche specific adaptations. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Insulin acutely triggers transcription of Slc2a4 gene: participation of the AT-rich, E-box and NFKB-binding sites.

    PubMed

    Moraes, Paulo Alexandre; Yonamine, Caio Yogi; Pinto Junior, Danilo Correa; Esteves, João Victor DelConti; Machado, Ubiratan Fabres; Mori, Rosana Cristina

    2014-09-26

    The insulin-sensitive glucose transporter protein GLUT4 (solute carrier family 2 member 4 (Slc2a4) gene) plays a key role in glycemic homeostasis. Decreased GLUT4 expression is a current feature in insulin resistant conditions such as diabetes, and the restoration of GLUT4 content improves glycemic control. This study investigated the effect of insulin upon Slc2a4/GLUT4 expression, focusing on the AT-rich element, E-box and nuclear factor NF-kappa-B (NFKB) site. Rat soleus muscles were incubated during 180 min with insulin, added or not with wortmannin (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (PI3K)-inhibitor), ML9 (serine/threonine protein kinase (AKT) inhibitor) and tumor necrosis factor (TNF, GLUT4 repressor), and processed for analysis of GLUT4 protein (Western blotting); Slc2a4, myocyte enhancer factor 2a/d (Mef2a/d), hypoxia inducible factor 1a (Hif1a), myogenic differentiation 1 (Myod1) and nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (Nfkb1) messenger ribonucleic acids (mRNAs) (polymerase chain reaction (PCR)); and AT-rich- (myocyte-specific enhancer factor 2 (MEF2)-binding site), E-box- (hypoxia inducible factor 1 alpha (HIF1A)- and myoblast determination protein 1 (MYOD1)-binding site), and NFKB-binding activity (electrophoretic mobility assay). Insulin increased Slc2a4 mRNA expression (140%) and nuclear proteins binding to AT-rich and E-box elements (~90%), all effects were prevented by wortmannin and ML9. Insulin also increased Mef2a/d and Myod1 mRNA expression, suggesting the participation of these transcriptional factors in the Slc2a4 enhancing effect. Conversely, insulin decreased Nfkb1 mRNA expression and protein binding to the NFKB-site (~50%). Furthermore, TNF-induced inhibition of GLUT4 expression (~40%) was prevented by insulin in an NFKB-binding repressing mechanism. GLUT4 protein paralleled the Slc2a4 mRNA regulations. Insulin enhances the Slc2a4/GLUT4 expression in the skeletal

  19. The Bluejay genome browser.

    PubMed

    Soh, Jung; Gordon, Paul M K; Sensen, Christoph W

    2012-03-01

    The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca.

  20. Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

    USGS Publications Warehouse

    Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

    2016-01-01

    The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

  1. Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and Plants is accepted for publication in MPMI

    SciTech Connect

    Karpinets, Tatiana V; Park, Byung H; Syed, Mustafa H; Klotz, Martin G; Uberbacher, Edward C

    2014-01-01

    Most bacterial symbionts of plants are phenotypically characterized by their parasitic or matualistic relationship with the host; however, the genomic characteristics that likely discriminate mutualistic symbionts from pathogens of plants are poorly understood. This study comparatively analyzed the genomes of 54 plant-symbiontic bacteria, 27 mutualists and 27 pathogens, to discover genomic determinants of their parasitic and mutualistic nature in terms of protein family domains, KEGG orthologous groups, metabolic pathways and families of carbohydrate-active enzymes (CAZymes). We further used all bacteria with sequenced genomesl, published microarrays and transcriptomics experimental datasets, and literature to validate and to explore results of the comparison. The analysis revealed that genomes of mutualists are larger in size and higher in GC content and encode greater molecular, functional and metabolic diversity than the investigated genomes of pathogens. This enriched molecular and functional enzyme diversity included constructive biosynthetic signatures of CAZymes and metabolic pathways in genomes of mutualists compared with catabolic signatures dominant in the genomes of pathogens. Another discriminative characteristic of mutualists is the co-occurence of gene clusters required for the expression and function of nitrogenase and RuBisCO. Analysis of previously published experimental data indicate that nitrogen-fixing mutualists may employ Rubisco to fix CO2 not in the canonical Calvin-Benson-Basham cycle but in a novel metabolic pathway, here called Rubisco-based glycolysis , to increase efficiency of sugar utilization during the symbiosis with plants. An important discriminative characteristic of plant pathogenic bacteria is two groups of genes likely encoding effector proteins involved in host invasion and a genomic locus encoding a putative secretion system that includes a DUF1525 domain protein conserved in pathogens of plants and of other organisms. The

  2. On the molecular mechanism of GC content variation among eubacterial genomes

    PubMed Central

    2012-01-01

    Background As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits), according to a hypothesis where GC content variation is essentially governed by genome replication and DNA repair mechanisms. Further investigation led to the discovery that two major mutator genes, polC and dnaE2, may be responsible for genomic GC content variation. Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes. Results Mutator genes, especially those with dominant effects on the mutation spectra, are biased towards either GC or AT richness, and they alter genomic GC content in the two opposite directions. Increased bacterial genome size (or gene number) appears to rely on increased genomic GC content; however, it is unclear whether the changes are directly related to certain environmental pressures. Certain environmental and bacteriological features are related to GC content variation, but their trends are more obvious when analyzed under the dnaE-based grouping scheme. Most terrestrial, plant-associated, and nitrogen-fixing bacteria are members of the dnaE1|dnaE2 group, whereas most pathogenic or symbiotic bacteria in insects, and those dwelling in aquatic environments, are largely members of the dnaE1|polV group. Conclusion Our studies provide several lines of evidence indicating that DNA polymerase III α subunit and its isoforms participating in either replication (such as polC) or SOS mutagenesis/translesion synthesis (such as dnaE2), play dominant roles in determining GC variability. Other environmental or bacteriological factors, such

  3. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease.

    PubMed

    Cooper, David N; Bacolla, Albino; Férec, Claude; Vasquez, Karen M; Kehrer-Sawatzki, Hildegard; Chen, Jian-Min

    2011-10-01

    Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease. © 2011 Wiley-Liss, Inc.

  4. A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

    PubMed Central

    2012-01-01

    Background The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach. Results The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides. PMID:22958331

  5. The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

    SciTech Connect

    Spring, Stefan; Scheuner, Carmen; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Nolan, Matt; Saunders, Elizabeth H; Pitluck, Samuel; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Lykidis, A; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia D; Goodwin, Lynne A.; Detter, J. Chris; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpidis, Nikos C; Klenk, Hans-Peter

    2010-12-01

    Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

  6. The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

    DOE PAGES

    Spring, Stefan; Scheuner, Carmen; Lapidus, Alla; ...

    2010-01-01

    Methanohalophilus mahii is the type species of the genus Methanohalophilus , which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP T was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of themore » reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.« less

  7. The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

    PubMed Central

    Spring, Stefan; Scheuner, Carmen; Lapidus, Alla; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Nolan, Matt; Saunders, Elizabeth; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Lykidis, Athanasios; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Goodwin, Lynne; Detter, John C.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species. PMID:21234345

  8. The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

    SciTech Connect

    Spring, Stefan; Scheuner, Carmen; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Nolan, Matt; Saunders, Elizabeth H; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Lykidis, A; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Goodwin, Lynne A.; Detter, J. Chris; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

  9. Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: the Genes-environments & Admixture in Latino Americans study.

    PubMed

    Galanter, Joshua M; Gignoux, Christopher R; Torgerson, Dara G; Roth, Lindsey A; Eng, Celeste; Oh, Sam S; Nguyen, Elizabeth A; Drake, Katherine A; Huntsman, Scott; Hu, Donglei; Sen, Saunak; Davis, Adam; Farber, Harold J; Avila, Pedro C; Brigino-Buenaventura, Emerita; LeNoir, Michael A; Meade, Kelley; Serebrisky, Denise; Borrell, Luisa N; Rodríguez-Cintrón, William; Estrada, Andres Moreno; Mendoza, Karla Sandoval; Winkler, Cheryl A; Klitz, William; Romieu, Isabelle; London, Stephanie J; Gilliland, Frank; Martinez, Fernando; Bustamante, Carlos; Williams, L Keoki; Kumar, Rajesh; Rodríguez-Santana, José R; Burchard, Esteban G

    2014-08-01

    Asthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations, and replication of positive associations has been inconsistent. We sought to identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping. Latino children with asthma (n = 1893) and healthy control subjects (n = 1881) were recruited from 5 sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci. We identified a significant association between ancestry and asthma at 6p21 (lowest P value: rs2523924, P < 5 × 10(-6)). This association replicates in a meta-analysis of the EVE Asthma Consortium (P = .01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between SNPs in the 17q21 region and asthma in Latinos (IKZF3, lowest P value: rs90792, odds ratio, 0.67; 95% CI, 0.61-0.75; P = 6 × 10(-13)) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies. Admixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, whereas genome-wide association confirms the previously identified locus on 17q21. Published by Mosby, Inc.

  10. Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs

    USDA-ARS?s Scientific Manuscript database

    One of the most important applications of genomic selection in maize breeding is to predict and identify the best-untested individuals from bi-parental populations, when the training and validation sets are derived from the same cross. Nineteen tropical maize bi-parental populations evaluated in mul...

  11. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  12. [Landscape and ecological genomics].

    PubMed

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

  13. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

    PubMed Central

    2010-01-01

    Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen. PMID:20398413

  14. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana.

    PubMed

    Roy, Adrita; Dutta, Arkajyoti; Roy, Dipan; Ganguly, Payel; Ghosh, Ritesh; Kar, Rajiv K; Bhunia, Anirban; Mukhopadhyay, Jayanta; Chaudhuri, Shubho

    2016-10-01

    ARID-HMG DNA-binding proteins represent a novel group of HMG-box containing protein family where the AT-rich interaction domain (ARID) is fused with the HMG-box domain in a single polypeptide chain. ARID-HMG proteins are highly plant specific with homologs found both in flowering plants as well as in moss such as Physcomitrella. The expression of these proteins is ubiquitous in plant tissues and primarily localises in the cell nucleus. HMGB proteins are involved in several nuclear processes, but the role of ARID-HMG proteins in plants remains poorly explored. Here, we performed DNA-protein interaction studies with Arabidopsis ARID-HMG protein HMGB11 (At1g55650) to understand the functionality of this protein and its individual domains. DNA binding assays revealed that AtHMGB11 can bind double-stranded DNA with a weaker affinity (Kd = 475 ± 17.9 nM) compared to Arabidopsis HMGB1 protein (Kd = 39.8 ± 2.68 nM). AtHMGB11 also prefers AT-rich DNA as a substrate and shows structural bias for supercoiled DNA. Molecular docking of the DNA-AtHMGB11 complex indicated that the protein interacts with the DNA major groove, mainly through its ARID domain and the junction region connecting the ARID and the HMG-box domain. Also, predicted by the docking model, mutation of Lys(85) from the ARID domain and Arg(199) & Lys(202) from the junction region affects the DNA binding affinity of AtHMGB11. In addition, AtHMGB11 and its truncated form containing the HMG-box domain can not only promote DNA mini-circle formation but are also capable of inducing negative supercoils into relaxed plasmid DNA suggesting the involvement of this protein in several nuclear events. Overall, the study signifies that both the ARID and the HMG-box domain contribute to the optimal functioning of ARID-HMG protein in vivo.

  15. Genomic Insights into Bifidobacteria

    PubMed Central

    Lee, Ju-Hoon; O'Sullivan, Daniel J.

    2010-01-01

    Summary: Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments. PMID:20805404

  16. The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

    PubMed Central

    Cook, Charles E

    2005-01-01

    Background Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum. Results I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda). This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness. Conclusion The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other Malacostraca show that all

  17. Synthesis and photophysical evaluation of a pyridinium 4-amino-1,8-naphthalimide derivative that upon intercalation displays preference for AT-rich double-stranded DNA.

    PubMed

    Banerjee, Swagata; Kitchen, Jonathan A; Gunnlaugsson, Thorfinnur; Kelly, John M

    2012-04-21

    The synthesis, characterisation and solid state crystal structure of a cationic 4-amino-1,8-naphthalimide derivative (1) are described. The photophysical properties of 1 are shown to vary with the solvent polarity and H-bonding ability. The fluorescence of 1 is enhanced and blue-shifted in its 1:1 complex with 5'-adenosine-monophosphate while it is partially quenched and red-shifted in its complex with 5'-guanosine-monophosphate. Linear and circular dichroism measurements show that 1 binds to double-stranded DNA by intercalation. Comparative UV-visible and fluorescence studies with double stranded synthetic polynucleotides poly(dA-dT)(2) and poly(dG-dC)(2) show that 1 binds much more strongly to the AT polymer; 1 also has a strong preference for A-T rich sequences in natural DNA. Thermal denaturation measurements also reveal a much greater stabilisation of the double-stranded poly(dA-dT)(2) than of natural DNA. This journal is © The Royal Society of Chemistry 2012

  18. Expression of tetanus toxin fragment C in yeast: gene synthesis is required to eliminate fortuitous polyadenylation sites in AT-rich DNA.

    PubMed Central

    Romanos, M A; Makoff, A J; Fairweather, N F; Beesley, K M; Slater, D E; Rayment, F B; Payne, M M; Clare, J J

    1991-01-01

    Fragment C is a non-toxic 50 kDa fragment of tetanus toxin which is a candidate subunit vaccine against tetanus. The AT-rich Clostridium tetani DNA encoding fragment C could not be expressed in Saccharomyces cerevisiae due to the presence of several fortuitous polyadenylation sites which gave rise to truncated mRNAs. The polyadenylation sites were eliminated by chemically synthesising the DNA with increased GC-content (from 29% to 47%). Synthesis of the entire gene (1400 base pairs) was necessary to generate full-length transcripts and for protein production in yeast. Using a GAL1 promoter vector, fragment C was expressed to 2-3% of soluble cell protein. Fragment C could also be secreted using the alpha-factor leader peptide as a secretion signal. The protein was present at 5-10 mg/l in the culture medium in two forms: a high molecular mass hyper-glycosylated protein (75-200 kDa) and a core-glycosylated protein (65 kDa). Intracellular fragment C was as effective in vaccinating mice against tetanus authentic fragment C. The glycosylated material was inactive, though it was rendered fully active by de-glycosylation. Images PMID:2027754

  19. The AT-rich tract of the SV40 ori core: negative synergism and specific recognition by single stranded and duplex DNA binding proteins.

    PubMed Central

    Galli, I; Iguchi-Ariga, S M; Ariga, H

    1992-01-01

    The SV40 origin of replication comprises a run of thymine and adenine residues. Integrity of this AT-rich sequence is known to be essential for replication. We set out to study whether or not these elements can work synergistically to sustain replication. Quite surprisingly, additional copies of the AT stretch linked to a functional SV40 ori core dramatically reduce its replication in Cosl cells, probably by creating some physical block. Interestingly, the same inhibiting effect can be observed with the addition in cis of the yeast ARS consensus, which is homologous to the SV40 AT stretch. This modulation is possibly due to the action of cellular factors that recognize either of the two sequences. In fact, we demonstrate the existence of factor(s) in Cosl crude nuclear extracts that in vitro can specifically bind to either of them. Moreover, we show that these sequence-specific factor(s) (MW about 50 kDa), named SOAP, recognize both single (T-rich strand) and double stranded forms of the AT tracts. Binding to single stranded AT stretches can be specifically inhibited by the corresponding duplex form, but not vice versa. Images PMID:1321411

  20. Host–Environment Medicine

    PubMed Central

    Rabinowitz, Peter M; Poljak, Alex

    2003-01-01

    Rapid developments in genomic and proteomic testing promise to impact the way in which clinicians assess disease risk and drug selection in their patients. Because most diseases result from host–environment interactions, however, primary care providers will need to avoid the trap of biological determinism by examining the important role of environmental factors in their clinical assessments and interventions. This article discusses the application of host–environment concepts to recent developments in the areas of genomics and proteomics. PMID:12648255

  1. Genome-Wide Gene-Environment Study Identifies Glutamate Receptor Gene GRIN2A as a Parkinson's Disease Modifier Gene via Interaction with Coffee

    PubMed Central

    Hamza, Taye H.; Chen, Honglei; Hill-Burns, Erin M.; Rhodes, Shannon L.; Montimurro, Jennifer; Kay, Denise M.; Tenesa, Albert; Kusel, Victoria I.; Sheehan, Patricia; Eaaswarkhanth, Muthukrishnan; Yearout, Dora; Samii, Ali; Roberts, John W.; Agarwal, Pinky; Bordelon, Yvette; Park, Yikyung; Wang, Liyong; Gao, Jianjun; Vance, Jeffery M.; Kendler, Kenneth S.; Bacanu, Silviu-Alin; Scott, William K.; Ritz, Beate; Nutt, John; Factor, Stewart A.; Zabetian, Cyrus P.; Payami, Haydeh

    2011-01-01

    Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P2df = 10−6, GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10−7) but not in light coffee-drinkers. The a priori Replication hypothesis that “Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers” was confirmed: ORReplication = 0.59, PReplication = 10−3; ORPooled = 0.51, PPooled = 7×10−8. Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10−3), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10−13). Imputation revealed a block of SNPs that achieved P2df<5×10−8 in GWAIS, and OR = 0.41, P = 3×10−8 in heavy coffee-drinkers. This study is proof of concept

  2. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Baker, Scott E.; Thykaer, Jette; Adney, William S.; Brettin, T.; Brockman, Fred J.; D'haeseleer, Patrik; Martinez, Antonio D.; Miller, R. M.; Rokhsar, Daniel S.; Schadt, Christopher W.; Torok, Tamas; Tuskan, Gerald; Bennett, Joan W.; Berka, Randy; Briggs, Steve; Heitman, Joseph; Taylor, John; Turgeon, Barbara G.; Werner-Washburne, Maggie; Himmel, Michael E.

    2008-09-30

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions.

  3. Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

    PubMed

    Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

    2008-08-01

    Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

  4. Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee.

    PubMed

    Hamza, Taye H; Chen, Honglei; Hill-Burns, Erin M; Rhodes, Shannon L; Montimurro, Jennifer; Kay, Denise M; Tenesa, Albert; Kusel, Victoria I; Sheehan, Patricia; Eaaswarkhanth, Muthukrishnan; Yearout, Dora; Samii, Ali; Roberts, John W; Agarwal, Pinky; Bordelon, Yvette; Park, Yikyung; Wang, Liyong; Gao, Jianjun; Vance, Jeffery M; Kendler, Kenneth S; Bacanu, Silviu-Alin; Scott, William K; Ritz, Beate; Nutt, John; Factor, Stewart A; Zabetian, Cyrus P; Payami, Haydeh

    2011-08-01

    Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P(2df) = 10(-6), GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10(-7)) but not in light coffee-drinkers. The a priori Replication hypothesis that "Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers" was confirmed: OR(Replication) = 0.59, P(Replication) = 10(-3); OR(Pooled) = 0.51, P(Pooled) = 7×10(-8). Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10(-3)), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10(-13)). Imputation revealed a block of SNPs that achieved P(2df)<5×10(-8) in GWAIS, and OR = 0.41, P = 3×10(-8) in heavy coffee-drinkers. This study is proof of

  5. Gene × environment interaction by a longitudinal epigenome-wide association study (LEWAS) overcomes limitations of genome-wide association study (GWAS).

    PubMed

    Lahiri, Debomoy K; Maloney, Bryan

    2012-12-01

    The goal of genome-wide association studies is to identify SNPs unique to disease. It usually involves a single sampling from subjects' lifetimes. While primary DNA sequence variation influences gene-expression levels, expression is also influenced by epigenetics, including the 'somatic epitype' (G(SE)), an epigenotype acquired postnatally. While genes are inherited, and novel polymorphisms do not routinely appear, G(SE) is fluid. Furthermore, G(SE) could respond to environmental factors (such as heavy metals) and to differences in exercise, maternal care and dietary supplements - all of which postnatally modify oxidation or methylation of DNA, leading to altered gene expression. Change in epigenetic status may be critical for the development of many diseases. We propose a 'longitudinal epigenome-wide association study', wherein G(SE) are measured at multiple time points along with subjects' histories. This Longitudinal epigenome-wide association study, based on the 'dynamic' somatic epitype over the 'static' genotype, merits further investigation.

  6. Identification of a genetic variant at 2q12.1 associated with blood pressure in East Asians by genome-wide scan including gene-environment interactions.

    PubMed

    Kim, Yun Kyoung; Kim, Youngdoe; Hwang, Mi Yeong; Shimokawa, Kazuro; Won, Sungho; Kato, Norihiro; Tabara, Yasuharu; Yokota, Mitsuhiro; Han, Bok-Ghee; Lee, Jong Ho; Kim, Bong-Jo

    2014-06-05

    Genome-wide association studies have identified many genetic loci associated with blood pressure (BP). Genetic effects on BP can be altered by environmental exposures via multiple biological pathways. Especially, obesity is one of important environmental risk factors that can have considerable effect on BP and it may interact with genetic factors. Given that, we aimed to test whether genetic factors and obesity may jointly influence BP. We performed meta-analyses of genome-wide association data for systolic blood pressure (SBP) and diastolic blood pressure (DBP) that included analyses of interaction between single nucleotide polymorphisms (SNPs) and the obesity-related anthropometric measures, body mass index (BMI), height, weight, and waist/hip ratio (WHR) in East-Asians (n = 12,030). We identified that rs13390641 on 2q12.1 demonstrated significant association with SBP when the interaction between SNPs and BMI was considered (P < 5 × 10 -8). The gene located nearest to rs13390641, TMEM182, encodes transmembrane protein 182. In stratified analyses, the effect of rs13390641 on BP was much stronger in obese individuals (BMI ≥ 30) than non-obese individuals and the effect of BMI on BP was strongest in individuals with the homozygous A allele of rs13390641. Our analyses that included interactions between SNPs and environmental factors identified a genetic variant associated with BP that was overlooked in standard analyses in which only genetic factors were included. This result also revealed a potential mechanism that integrates genetic factors and obesity related traits in the development of high BP.

  7. Bacteriophage T4 genome.

    PubMed

    Miller, Eric S; Kutter, Elizabeth; Mosig, Gisela; Arisaka, Fumio; Kunisawa, Takashi; Rüger, Wolfgang

    2003-03-01

    Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex

  8. Chromatin remodeling gene AT-rich interactive domain-containing protein 1A suppresses gastric cancer cell proliferation by targeting PIK3CA and PDK1

    PubMed Central

    Wang, Jie; Cui, Shu-Jian; Wang, Xiao-Qing; Jiang, Ying-Hua; Feng, Li; Yang, Peng-Yuan; Liu, Feng

    2016-01-01

    The tumor suppressor gene AT-rich interactive domain-containing protein 1A (ARID1A) was frequently mutated in cancers. The modulation mechanism of ARID1A for PI3K/AKT signaling in gastric cancer (GC) remains elusive. Here, we found that depletion of endogenous ARID1A enhanced the in vitro proliferation, colony formation, cellular growth, nutrient uptake and in vivo xenograft tumor growth of GC cells. PI3K/AKT activation by ARID1A-silencing was profiled using a phospho-protein antibody array. The phosphorylation of PDK1, AKT, GSK3β and 70S6K, and the protein and mRNA expressions of PI3K and PDK1, were upregulated by ARID1A-silencing. Chromatin immunoprecipitation and luciferase reporter assay revealed that ARID1A-involved SWI/SNF complex inhibited PIK3CA and PDK1 transcription by direct binding to their promoters. Serial deletion mutation analyses revealed that the ARID1A central region containing the HIC1-binding domain, but not the ARID DNA-binding domain and the C-terminal domain, was essential for the inhibition of GC cell growth, PI3K/AKT pathway phosphorylation and its transcriptional modulation activity of PIK3CA and PDK1. The proliferation, cellular growth and glucose consumption of ARID1A-deficient GC cells were efficiently prohibited by allosteric inhibitors mk2206 and LY294002, which targeting AKT and PI3K, respectively. Both inhibitors also downregulated the phosphorylation of PI3K/AKT pathway in ARID1A-deficient GC cells. Such cells were sensitized to the treatment of LY294002, and AT7867, another inhibitor of AKT and p70S6K. The administration of LY294002 alone inhibited the in vivo growth of ARID1A- deficient GC cells in mouse xenograft model. Our study provides a novel insight into the modulatory function and mechanism of ARID1A in PI3K/AKT signaling in GC. PMID:27323812

  9. Over-expression of the special AT rich sequence binding protein 1 (SATB1) promotes the progression of nasopharyngeal carcinoma: association with EBV LMP-1 expression

    PubMed Central

    2013-01-01

    Background Special AT rich sequence binding protein 1 (SATB1) plays a crucial role in the biology of various types of human cancer. However, the role of SATB1 in human nasopharyngeal carcinoma (NPC) remains unknown. In the present study, we sought to investigate the contribution of aberrant SATB1 expression in the progression of NPC and its association with the Epstein Barr virus (EBV)-encoded latent membrane protein 1 (LMP-1). Methods Immunohistochemical analysis was performed to detect SATB1 and LMP-1 protein in clinical samples, and the association of SATB1 protein expression with patient clinicopathological characteristics and LMP-1 expression were analyzed. SATB1 expression profiles were evaluated in well-differentiated NPC cell line CNE1, poorly-differentiated CNE2Z, undifferentiated C666-1 and immortalized nasopharyngeal epithelia NP-69 cells using quantitative RT-PCR, western blotting and fluorescent staining. After inhibition the SATB1 expression by using SATB1 specific small interfering RNA in these cell lines, the change of cell proliferation was investigated by western blotting analysis of PCNA (proliferating cell nuclear antigen) expression and CCK-8 assay, and the cell migration was assessed by Transwell migration assay. Finally, the expressions of SATB1 and PCNA were examined in CNE1 cells that forced LMP-1 expression by fluorescent staining and RT-PCR. Results Immunohistochemical analysis revealed that SATB1 protein expression was elevated in NPC tissues compared to benign nasopharyngeal tissues (P = 0.005). Moreover, high levels of SATB1 protein expression were positively correlated with clinical stage (P = 0.025), the status of lymph node metastasis (N classification) (P = 0.018), distant metastasis (M classification) (P = 0.041) and LMP-1 expression status (r = 2.35, P < 0.01) in NPC patients. In vitro experiments demonstrated that an inverse relationship between SATB1 expression and NPC differentiation status, with SATB1

  10. Sequence and organization of complete mitochondrial genome of the firefly, Aquatica leii (Coleoptera: Lampyridae).

    PubMed

    Jiao, Hengwu; Ding, Minghui; Zhao, Huabin

    2015-01-01

    The firefly Aquatica leii (Coleoptera: Lampyridae) is widely distributed in China. In this study, we sequenced and characterized the first complete mitochondrial genome of the firefly from the subfamily Luciolinae. The circular genome of 16,856 bp in length contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. Overall base composition of the genome is 42.28% A, 34.80% T, 13.91% C and 9.01% G, with an AT bias of 77.08%. All protein-coding genes start with an ATN codon, and terminate with the typical stop codon TAA, TAG or a single T. The non-coding AT-rich region is unusually long (2239 bp), containing six 113 bp tandem repeats and a microsatellite-like (TA)7 element. The genome sequence is useful for studying the evolution of sexual signaling and many ecological specializations in fireflies.

  11. Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations

    USDA-ARS?s Scientific Manuscript database

    The genome sequence of the phytopathogenic fungus Leptosphaeria maculans has been determined. It has a unique bipartite structure, divided between distinct GC-equilibrated and AT-rich regions (isochores), reminiscent of some plants and animals but not previously observed in fungi. The GC-equilibrate...

  12. The Genome of the Moderate Halophile Amycolicicoccus subflavus DQS3-9A1T Reveals Four Alkane Hydroxylation Systems and Provides Some Clues on the Genetic Basis for Its Adaptation to a Petroleum Environment

    PubMed Central

    Nie, Yong; Fang, Hui; Li, Yan; Chi, Chang-Qiao; Tang, Yue-Qin; Wu, Xiao-Lei

    2013-01-01

    The moderate halophile Amycolicicoccus subflavus DQS3-9A1T is the type strain of a novel species in the recently described novel genus Amycolicicoccus, which was isolated from oil mud precipitated from oil produced water. The complete genome of A. subflavus DQS3-9A1T has been sequenced and is characteristic of harboring the genes for adaption to the harsh petroleum environment with salinity, high osmotic pressure, and poor nutrient levels. Firstly, it characteristically contains four types of alkane hydroxylases, including the integral-membrane non-heme iron monooxygenase (AlkB) and cytochrome P450 CYP153, a long-chain alkane monooxygenase (LadA) and propane monooxygenase. It also accommodates complete pathways for the response to osmotic pressure. Physiological tests proved that the strain could grow on n-alkanes ranging from C10 to C36 and propane as the sole carbon sources, with the differential induction of four kinds of alkane hydroxylase coding genes. In addition, the strain could grow in 1–12% NaCl with the putative genes responsible for osmotic stresses induced as expected. These results reveal the effective adaptation of the strain DQS3-9A1T to harsh oil environment and provide a genome platform to investigate the global regulation of different alkane metabolisms in bacteria that are crucially important for petroleum degradation. To our knowledge, this is the first report to describe the co-existence of such four types of alkane hydroxylases in a bacterial strain. PMID:23967144

  13. The genome of the moderate halophile Amycolicicoccus subflavus DQS3-9A1(T) reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment.

    PubMed

    Nie, Yong; Fang, Hui; Li, Yan; Chi, Chang-Qiao; Tang, Yue-Qin; Wu, Xiao-Lei

    2013-01-01

    The moderate halophile Amycolicicoccus subflavus DQS3-9A1(T) is the type strain of a novel species in the recently described novel genus Amycolicicoccus, which was isolated from oil mud precipitated from oil produced water. The complete genome of A. subflavus DQS3-9A1(T) has been sequenced and is characteristic of harboring the genes for adaption to the harsh petroleum environment with salinity, high osmotic pressure, and poor nutrient levels. Firstly, it characteristically contains four types of alkane hydroxylases, including the integral-membrane non-heme iron monooxygenase (AlkB) and cytochrome P450 CYP153, a long-chain alkane monooxygenase (LadA) and propane monooxygenase. It also accommodates complete pathways for the response to osmotic pressure. Physiological tests proved that the strain could grow on n-alkanes ranging from C10 to C36 and propane as the sole carbon sources, with the differential induction of four kinds of alkane hydroxylase coding genes. In addition, the strain could grow in 1-12% NaCl with the putative genes responsible for osmotic stresses induced as expected. These results reveal the effective adaptation of the strain DQS3-9A1(T) to harsh oil environment and provide a genome platform to investigate the global regulation of different alkane metabolisms in bacteria that are crucially important for petroleum degradation. To our knowledge, this is the first report to describe the co-existence of such four types of alkane hydroxylases in a bacterial strain.

  14. The complete mitochondrial genome of Tetrastemma olgarum (Nemertea: Hoplonemertea).

    PubMed

    Sun, Wen-Yan; Shen, Chun-Yang; Sun, Shi-Chun

    2016-01-01

    The complete mitochondrial genome (mitogenome) of Tetrastemma olgarum is sequenced. It is 14,580 bp in length and contains 37 genes typical for metazoan mitogenomes. The gene order is identical to that of the previously published Hoplonemertea mitogenomes. All genes are encoded on the heavy strand except for trnT and trnP. The coding strand is AT-rich, accounting for 69.2% of overall nucleotide composition.

  15. 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

  16. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

    PubMed

    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.

  17. Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments.

    PubMed

    Torregrosa-Crespo, Javier; González-Torres, Pedro; Bautista, Vanesa; Esclapez, Julia M; Pire, Carmen; Camacho, Mónica; Bonete, María José; Richardson, David J; Watmough, Nicholas J; Martínez-Espinosa, Rosa María

    2017-09-19

    Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Whilst the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management. This article is protected by copyright. All rights reserved. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. Gene × environment interaction by a longitudinal epigenome-wide association study (LEWAS) overcomes limitations of genome-wide association study (GWAS)

    PubMed Central

    Lahiri, Debomoy K; Maloney, Bryan

    2013-01-01

    The goal of genome-wide association studies is to identify SNPs unique to disease. It usually involves a single sampling from subjects' lifetimes. While primary DNA sequence variation influences gene-expression levels, expression is also influenced by epigenetics, including the ‘somatic epitype’ (GSE), an epigenotype acquired postnatally. While genes are inherited, and novel polymorphisms do not routinely appear, GSE is fluid. Furthermore, GSE could respond to environmental factors (such as heavy metals) and to differences in exercise, maternal care and dietary supplements – all of which postnatally modify oxidation or methylation of DNA, leading to altered gene expression. Change in epigenetic status may be critical for the development of many diseases. We propose a ‘longitudinal epigenome-wide association study’, wherein GSE are measured at multiple time points along with subjects' histories. This Longitudinal epigenome-wide association study, based on the ‘dynamic’ somatic epitype over the ‘static’ genotype, merits further investigation. PMID:23244313

  19. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment.

    PubMed

    Zhang, Bo; Zhang, Yan-Hong; Wang, Xin; Zhang, Hui-Xian; Lin, Qiang

    2017-07-01

    The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep-sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein-coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon-like noncanonical open reading frames (ORFs), and a control region-like (CR-like) element. All of the mitochondrial genes were coded by the same strand (the H-strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep-sea environment.

  20. Prophage Genomics

    PubMed Central

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria. PMID:12794192

  1. Genome-wide Association with C-Reactive Protein Levels in CLHNS: Evidence for the CRP and HNF1A Loci and their Interaction with exposure to a pathogenic environment

    PubMed Central

    Wu, Ying; McDade, Thomas W.; Kuzawa, Christopher W.; Borja, Judith; Li, Yun; Adair, Linda S.; Mohlke, Karen L.; Lange, Leslie A.

    2011-01-01

    Recent genome-wide association (GWA) studies have related several genetic loci, including CRP, HNF1A and LEPR, to circulating C-reactive protein (CRP) levels in populations of European ancestry. The genetic effects in other populations and across varying levels of exposure to a pathogenic environment, an important environmental factor associated with CRP, remain to be determined. We tested 2,073,674 SNPs for association with plasma CRP (limited to ≤ 10 mg/L) in 1,709 unrelated Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The strongest evidence of association was observed with variants at CRP (rs876537, P = 1.4 × 10−9) and HNF1A (rs7305618, P = 1.0 × 10−8). Among other previously reported CRP associated loci, the APOE ε4 haplotype was associated with decreased CRP level (P = 7.1 × 10−4), and modest association was observed with LEPR (rs1892534, P = 0.076), with direction of effects consistent with previous studies. The strongest signal at a locus not previously reported mapped to a gene desert region on chromosome 6q16.1 (rs1408282, P = 2.9 × 10−6). Finally, we observed nominal evidence of interaction with exposure to a pathogenic environment for top main effect SNPs at HNF1A (rs7305618, P = 0.031), LEPR (rs1892535, P = 0.030) and 6q16.1 (rs1408282, P = 0.046). Our findings demonstrate convincing evidence that genetic variants in CRP and HNF1A contribute to plasma CRP in Filipino women, and provide the first evidence that exposure to a pathogenic environment may modify the genetic influence at the HNF1A, LEPR and 6q16.1 loci on plasma CRP level. PMID:21647738

  2. Aquaculture Genomics

    USDA-ARS?s Scientific Manuscript database

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  3. Genomics of Salmonella Species

    NASA Astrophysics Data System (ADS)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  4. Genomics for weed science.

    PubMed

    Horvath, David

    2010-03-01

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds.

  5. Genomics for Weed Science

    PubMed Central

    Horvath, David

    2010-01-01

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds. PMID:20808523

  6. Cloud computing for comparative genomics.

    PubMed

    Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

    2010-05-18

    Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

  7. Cloud computing for comparative genomics

    PubMed Central

    2010-01-01

    Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems. PMID:20482786

  8. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores

    PubMed Central

    Hiratani, Ichiro; Leskovar, Amanda; Gilbert, David M.

    2004-01-01

    The replication timing of some genes is developmentally regulated, but the significance of replication timing to cellular differentiation has been difficult to substantiate. Studies have largely been restricted to the comparison of a few genes in established cell lines derived from different tissues, and most of these genes do not change replication timing. Hence, it has not been possible to predict how many or what types of genes might be subject to such control. Here, we have evaluated the replication timing of 54 tissue-specific genes in mouse embryonic stem cells before and after differentiation to neural precursors. Strikingly, genes residing within isochores rich in GC and poor in long interspersed nuclear elements (LINEs) did not change their replication timing, whereas half of genes within isochores rich in AT and long interspersed nuclear elements displayed programmed changes in replication timing that accompanied changes in gene expression. Our results provide direct evidence that differentiation-induced autosomal replication-timing changes are a significant part of mammalian development, provide a means to predict genes subject to such regulation, and suggest that replication timing may be more related to the evolution of metazoan genomes than to gene function or expression pattern. PMID:15557005

  9. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores.

    PubMed

    Hiratani, Ichiro; Leskovar, Amanda; Gilbert, David M

    2004-11-30

    The replication timing of some genes is developmentally regulated, but the significance of replication timing to cellular differentiation has been difficult to substantiate. Studies have largely been restricted to the comparison of a few genes in established cell lines derived from different tissues, and most of these genes do not change replication timing. Hence, it has not been possible to predict how many or what types of genes might be subject to such control. Here, we have evaluated the replication timing of 54 tissue-specific genes in mouse embryonic stem cells before and after differentiation to neural precursors. Strikingly, genes residing within isochores rich in GC and poor in long interspersed nuclear elements (LINEs) did not change their replication timing, whereas half of genes within isochores rich in AT and long interspersed nuclear elements displayed programmed changes in replication timing that accompanied changes in gene expression. Our results provide direct evidence that differentiation-induced autosomal replication-timing changes are a significant part of mammalian development, provide a means to predict genes subject to such regulation, and suggest that replication timing may be more related to the evolution of metazoan genomes than to gene function or expression pattern.

  10. Phototroph genomics ten years on.

    PubMed

    Raymond, Jason; Swingley, Wesley D

    2008-07-01

    The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work--understandably skewed toward health-related disciplines--and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.

  11. Complete mitochondrial genome of brown marmorated stink bug Halyomorpha halys (Hemiptera: Pentatomidae) and phylogenetic relationships of Hemipteran suborders

    USDA-ARS?s Scientific Manuscript database

    The newly sequenced complete mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys (Stal) (Hemiptera: Pentatomidae), is a circular molecule of 16,518 bp with a total A+T content of 76.4% and two extensive repeat regions in A+T rich region. Nucleotide composition and codon usage ...

  12. Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes

    PubMed Central

    Sinoquet, Christine; Demey, Sylvain; Braun, Frédérique

    2008-01-01

    This article compares 32 bacterial genomes with respect to their high transcription potentialities. The σ70 promoter has been widely studied for Escherichia coli model and a consensus is known. Since transcriptional regulations are known to compensate for promoter weakness (i.e. when the promoter similarity with regard to the consensus is rather low), predicting functional promoters is a hard task. Instead, the research work presented here comes within the scope of investigating potentially high ORF expression, in relation with three criteria: (i) high similarity to the σ70 consensus (namely, the consensus variant appropriate for each genome), (ii) transcription strength reinforcement through a supplementary binding site—the upstream promoter (UP) element—and (iii) enhancement through an optimal Shine-Dalgarno (SD) sequence. We show that in the AT-rich Firmicutes’ genomes, frequencies of potentially strong σ70-like promoters are exceptionally high. Besides, though they contain a low number of strong promoters (SPs), some genomes may show a high proportion of promoters harbouring an UP element. Putative SPs of lesser quality are more frequently associated with an UP element than putative strong promoters of better quality. A meaningful difference is statistically ascertained when comparing bacterial genomes with similarly AT-rich genomes generated at random; the difference is the highest for Firmicutes. Comparing some Firmicutes genomes with similarly AT-rich Proteobacteria genomes, we confirm the Firmicutes specificity. We show that this specificity is neither explained by AT-bias nor genome size bias; neither does it originate in the abundance of optimal SD sequences, a typical and significant feature of Firmicutes more thoroughly analysed in our study. PMID:18440978

  13. The bat genome: GC-biased small chromosomes associated with reduction in genome size.

    PubMed

    Kasai, Fumio; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A

    2013-12-01

    Bats are distinct from other mammals in their small genome size as well as their high metabolic rate, possibly related to flight ability. Although the genome sequence has been published in two species, the data lack cytogenetic information. In this study, the size and GC content of each chromosome are measured from the flow karyotype of the mouse-eared bat, Myotis myotis (MMY). The smaller chromosomes are GC-rich compared to the larger chromosomes, and the relative proportions of homologous segments between MMY and human differ among the MMY chromosomes. The MMY genome size calculated from the sum of the chromosome sizes is 2.25 Gb, and the total GC content is 42.3%, compared to human and dog with 41.0 and 41.2%, respectively. The GC-rich small MMY genome is characterised by GC-biased smaller chromosomes resulting from preferential loss of AT-rich sequences. Although the association between GC-rich small chromosomes and small genome size has been reported only in birds so far, we show in this paper, for the first time, that the same phenomenon is observed in at least one group of mammals, implying that this may be a mechanism common to genome evolution in general.

  14. Whole genome plasticity in pathogenic bacteria.

    PubMed

    Dobrindt, U; Hacker, J

    2001-10-01

    The exploitation of bacterial genome sequences has so far provided a wealth of new general information about the genetic diversity of bacteria, such as that of many pathogens. Comparative genomics uncovered many genome variations in closely related bacteria and revealed basic principles involved in bacterial diversification, improving our knowledge of the evolution of bacterial pathogens. A correlation between metabolic versatility and genome size has become evident. The degenerated life styles of obligate intracellular pathogens correlate with significantly reduced genome sizes, a phenomenon that has been termed "evolution by reduction". These mechanisms can permanently alter bacterial genotypes and result in adaptation to their environment by genome optimization. In this review, we summarize the recent results of genome-wide approaches to studying the genetic diversity of pathogenic bacteria that indicate that the acquisition of DNA and the loss of genetic information are two important mechanisms that contribute to strain-specific differences in genome content.

  15. Cloning and characterization of a repetitive DNA detected by HindIII in the genome of Raja montagui (Batoidea, Chondrichthyes).

    PubMed

    Rocco, L; Stingo, V; Bellitti, M

    1996-10-17

    A repetitive HindIII fragment of DNA from Raja montagui (Rajiformes) was cloned and sequenced for the first time in cartilaginous fishes. This element, which comprises approximately 5% of the whole genome of the spotted ray, is absent in long tandem arrays, being typical of satellite DNA. It appeared constituted by 311 AT-rich bp (61%). The clone was hybridized to the genomic DNA of species with varying phyletic distances, revealing a high degree of conservation.

  16. Genome-wide association with C-reactive protein levels in CLHNS: evidence for the CRP and HNF1A loci and their interaction with exposure to a pathogenic environment.

    PubMed

    Wu, Ying; McDade, Thomas W; Kuzawa, Christopher W; Borja, Judith; Li, Yun; Adair, Linda S; Mohlke, Karen L; Lange, Leslie A

    2012-04-01

    Recent genome-wide association studies have related several genetic loci, including C-reactive protein (CRP), hepatocyte nuclear factor 1 homeobox (HNF1A), and genetic variations in the leptin receptor (LEPR), to circulating CRP levels in populations of European ancestry. The genetic effects in other populations and across varying levels of exposure to a pathogenic environment, an important environmental factor associated with CRP, remain to be determined. We tested 2,073,674 single-nucleotide polymorphisms (SNPs) for association with plasma CRP (limited to ≤10 mg/L) in 1,709 unrelated Filipino women from the Cebu Longitudinal Health and Nutrition Survey. The strongest evidence of association was observed with variants at CRP (rs876537, P = 1.4 × 10(-9)) and HNF1A (rs7305618, P = 1.0 × 10(-8)). Among other previously reported CRP-associated loci, the apolipoprotein E ε4 haplotype was associated with decreased CRP level (P = 7.1 × 10(-4)), and modest association was observed with LEPR (rs1892534, P = 0.076), with direction of effects consistent with previous studies. The strongest signal at a locus not previously reported mapped to a gene desert region on chromosome 6q16.1 (rs1408282, P = 2.9 × 10(-6)). Finally, we observed nominal evidence of interaction with exposure to a pathogenic environment for top main effect SNPs at HNF1A (rs7305618, P = 0.031), LEPR (rs1892535, P = 0.030) and 6q16.1 (rs1408282, P = 0.046). Our findings demonstrate convincing evidence that genetic variants in CRP and HNF1A contribute to plasma CRP in Filipino women and provide the first evidence that exposure to a pathogenic environment may modify the genetic influence at the HNF1A, LEPR, and 6q16.1 loci on plasma CRP level.

  17. The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae).

    PubMed

    Shao, Lili; Sun, QianQian; Hao, JiaSheng

    2015-01-01

    The mitochondrial genome (mitogenome) of Parara guttata (Hesperiidae: Hesperiinae) is a circular molecule of 15,441 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All PCGs start with a typical ATN codon except for COI and ND1 which use CGA and GTG as their start codons, respectively. Some PCGs harbor TAG (ND1) or incomplete termination codon T (COI, COII, ND5, ND4), while others use standard TAA as their termination codons. The 411-bp long AT-rich region contains a conserved motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)5 element preceded by the ATTTA motif.

  18. Fueling Future with Algal Genomics

    SciTech Connect

    Grigoriev, Igor

    2012-07-05

    Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  19. Hawaiian Drosophila genomes: size variation and evolutionary expansions.

    PubMed

    Craddock, Elysse M; Gall, Joseph G; Jonas, Mark

    2016-02-01

    This paper reports genome sizes of one Hawaiian Scaptomyza and 16 endemic Hawaiian Drosophila species that include five members of the antopocerus species group, one member of the modified mouthpart group, and ten members of the picture wing clade. Genome size expansions have occurred independently multiple times among Hawaiian Drosophila lineages, and have resulted in an over 2.3-fold range of genome sizes among species, with the largest observed in Drosophila cyrtoloma (1C = 0.41 pg). We find evidence that these repeated genome size expansions were likely driven by the addition of significant amounts of heterochromatin and satellite DNA. For example, our data reveal that the addition of seven heterochromatic chromosome arms to the ancestral haploid karyotype, and a remarkable proportion of ~70 % satellite DNA, account for the greatly expanded size of the D. cyrtoloma genome. Moreover, the genomes of 13/17 Hawaiian picture wing species are composed of substantial proportions (22-70 %) of detectable satellites (all but one of which are AT-rich). Our results suggest that in this tightly knit group of recently evolved species, genomes have expanded, in large part, via evolutionary amplifications of satellite DNA sequences in centric and pericentric domains (especially of the X and dot chromosomes), which have resulted in longer acrocentric chromosomes or metacentrics with an added heterochromatic chromosome arm. We discuss possible evolutionary mechanisms that may have shaped these patterns, including rapid fixation of novel expanded genomes during founder-effect speciation.

  20. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  1. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  2. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

    This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape. PMID:12750305

  3. Privacy in the Genomic Era

    PubMed Central

    NAVEED, MUHAMMAD; AYDAY, ERMAN; CLAYTON, ELLEN W.; FELLAY, JACQUES; GUNTER, CARL A.; HUBAUX, JEAN-PIERRE; MALIN, BRADLEY A.; WANG, XIAOFENG

    2015-01-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

  4. Privacy in the Genomic Era.

    PubMed

    Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng

    2015-09-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

  5. Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness

    PubMed Central

    2010-01-01

    Background Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC) libraries and expressed sequence tag (EST) libraries. Results 288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs. Conclusion The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physical and structural constraints, such as slippage of DNA replication machinery, that may generate increased allelic diversity in AT-rich sequence motifs. Although in silico approaches work well for SSR locus identification in both EST and BAC libraries, BAC library sequence and AT-rich repeat motifs are generally superior SSR development resources for most applications. PMID:20624300

  6. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts

    PubMed Central

    Newton, Irene L.G.; Clark, Michael E.; Kent, Bethany N.; Bordenstein, Seth R.; Qu, Jiaxin; Richards, Stephen; Kelkar, Yogeshwar D.; Werren, John H.

    2016-01-01

    Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm–egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor. Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia. Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and

  7. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts.

    PubMed

    Newton, Irene L G; Clark, Michael E; Kent, Bethany N; Bordenstein, Seth R; Qu, Jiaxin; Richards, Stephen; Kelkar, Yogeshwar D; Werren, John H

    2016-06-03

    Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm-egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and

  8. Genome mapping

    USDA-ARS?s Scientific Manuscript database

    Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as landmarks along the chromosome and provide researchers information as to how close they may be to a gene or region of inter...

  9. The complete mitochondrial genome of domestic sheep, Ovis aries.

    PubMed

    Hu, Xiao-di; Gao, Li-zhi

    2016-01-01

    In this study, we report a complete mitochondrial (mt) genome sequence of the Texel ewe, Ovis aries. The total genome is 16,615 bp in length and its overall base composition was estimated to be 33.68% for A, 27.36% for T, 25.86% for C, and 13.10% for G indicating an AT-rich (61.04%) feature in the O. aries mtgenome. It contains a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region (D-loop region). Comparisons with other publicly available sheep mitogenomes revealed a bunch of nucleotide diversity. This complete mitgenome sequence would enlarge useful genomic information for further studies on sheep evolution and domestication that will enhance germplasm conservation and breeding programs of O. aries.

  10. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans

    PubMed Central

    Shoguchi, Eiichi; Shinzato, Chuya; Hisata, Kanako; Satoh, Nori; Mungpakdee, Sutada

    2015-01-01

    Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures. PMID:26199191

  11. Population structure of mitochondrial genomes in Saccharomyces cerevisiae.

    PubMed

    Wolters, John F; Chiu, Kenneth; Fiumera, Heather L

    2015-06-11

    Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences. To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae. Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects.

  12. Apicoplast genome of the coccidian Eimeria tenella.

    PubMed

    Cai, Xiaomin; Fuller, A Lorraine; McDougald, Larry R; Zhu, Guan

    2003-12-04

    Unicellular apicomplexans possess an algal-originated plastid referred to as an apicoplast. Although apicomplexan parasites are comprised of highly diverse protists, the complete apicoplast genome sequences have only been determined from the hematozoan Plasmodium falciparum and cyst-forming coccidian Toxoplasma gondii. Here, we report the third complete sequence of apicoplast genome from the intestinal coccidian Eimeria tenella that may serve as a new drug target against coccidiosis in the livestock. The AT-rich E. tenella plastid genome is a 35-kb circular element. Its gene organization resembles more closely that of T. gondii than P. falciparum. Although the E. tenella plastid genome contains an almost identical set of genes to that found in P. falciparum and T. gondii, its encoded genes share low or moderate homologies with their counterparts in the other two apicomplexans. With the addition of this coccidian plastid genome sequence, we attempted to reexamine the apicoplast genome evolution and performed phylogenetic reconstructions using maximum likelihood and Bayesian inference (BI) methods based on a concatenated dataset of plastid-encoded rpoB, rpoC1 and rpoC2 proteins. All resulting rpo protein trees placed apicoplast as a sister to Euglena within the green lineage. On the other hand, many recent studies based on the organization of plastid genes and some nuclear-encoded plastid proteins have supported a common red algal ancestry of apicomplexan and dinoflagellate plastids. If the apicoplast indeed originated from a red ancestor, the green relationship of apicomplexan genes would probably imply that the ancestral host that gave rise to the (red) apicoplast might have already contained some primary green plastid genes.

  13. The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

    PubMed Central

    Qian, Jun; Song, Jingyuan; Gao, Huanhuan; Zhu, Yingjie; Xu, Jiang; Pang, Xiaohui; Yao, Hui; Sun, Chao; Li, Xian’en; Li, Chuyuan; Liu, Juyan; Xu, Haibin; Chen, Shilin

    2013-01-01

    Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant. PMID:23460883

  14. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.

    PubMed

    Qian, Jun; Song, Jingyuan; Gao, Huanhuan; Zhu, Yingjie; Xu, Jiang; Pang, Xiaohui; Yao, Hui; Sun, Chao; Li, Xian'en; Li, Chuyuan; Liu, Juyan; Xu, Haibin; Chen, Shilin

    2013-01-01

    Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.

  15. Complete mitochondrial genome sequence of Cheirotonus jansoni (Coleoptera: Scarabaeidae).

    PubMed

    Shao, L L; Huang, D Y; Sun, X Y; Hao, J S; Cheng, C H; Zhang, W; Yang, Q

    2014-02-20

    We sequenced the complete mitochondrial genome (mitogenome) of Cheirotonus jansoni (Coleoptera: Scarabaeidae), an endangered insect species from Southeast Asia. This long legged scarab is widely collected and reared for sale, although it is rare and protected in the wild. The circular genome is 17,249 bp long and contains a typical gene complement: 13 protein-coding genes, 2 rRNA genes, 22 putative tRNA genes, and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most insect mitogenomes. As with all other sequenced coleopteran species, a 5-bp long TAGTA motif was detected in the intergenic space sequence located between trnS(UCN) and nad1. The atypical cox1 start codon is AAC, and the putative initiation codon for the atp8 gene appears to be GTC, instead of the frequently found ATN. By sequence comparison, the 2590-bp long non-coding AT-rich region is the second longest among the coleopterans, with two tandem repeat regions: one is 10 copies of an 88-bp sequence and the other is 2 copies of a 153-bp sequence. Additionally, the A+T content (64%) of the 13 protein-coding genes is the lowest among all sequenced coleopteran species. This newly sequenced genome aids in our understanding of the comparative biology of the mitogenomes of coleopteran species and supplies important data for the conservation of this species.

  16. Personal genomics services: whose genomes?

    PubMed Central

    Gurwitz, David; Bregman-Eschet, Yael

    2009-01-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  17. A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera.

    PubMed

    Zayed, Amro; Whitfield, Charles W

    2008-03-04

    Apis mellifera originated in Africa and extended its range into Eurasia in two or more ancient expansions. In 1956, honey bees of African origin were introduced into South America, their descendents admixing with previously introduced European bees, giving rise to the highly invasive and economically devastating "Africanized" honey bee. Here we ask whether the honey bee's out-of-Africa expansions, both ancient and recent (invasive), were associated with a genome-wide signature of positive selection, detected by contrasting genetic differentiation estimates (F(ST)) between coding and noncoding SNPs. In native populations, SNPs in protein-coding regions had significantly higher F(ST) estimates than those in noncoding regions, indicating adaptive evolution in the genome driven by positive selection. This signal of selection was associated with the expansion of honey bees from Africa into Western and Northern Europe, perhaps reflecting adaptation to temperate environments. We estimate that positive selection acted on a minimum of 852-1,371 genes or approximately 10% of the bee's coding genome. We also detected positive selection associated with the invasion of African-derived honey bees in the New World. We found that introgression of European-derived alleles into Africanized bees was significantly greater for coding than noncoding regions. Our findings demonstrate that Africanized bees exploited the genetic diversity present from preexisting introductions in an adaptive way. Finally, we found a significant negative correlation between F(ST) estimates and the local GC content surrounding coding SNPs, suggesting that AT-rich genes play an important role in adaptive evolution in the honey bee.

  18. A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera

    PubMed Central

    Zayed, Amro; Whitfield, Charles W.

    2008-01-01

    Apis mellifera originated in Africa and extended its range into Eurasia in two or more ancient expansions. In 1956, honey bees of African origin were introduced into South America, their descendents admixing with previously introduced European bees, giving rise to the highly invasive and economically devastating “Africanized” honey bee. Here we ask whether the honey bee's out-of-Africa expansions, both ancient and recent (invasive), were associated with a genome-wide signature of positive selection, detected by contrasting genetic differentiation estimates (FST) between coding and noncoding SNPs. In native populations, SNPs in protein-coding regions had significantly higher FST estimates than those in noncoding regions, indicating adaptive evolution in the genome driven by positive selection. This signal of selection was associated with the expansion of honey bees from Africa into Western and Northern Europe, perhaps reflecting adaptation to temperate environments. We estimate that positive selection acted on a minimum of 852–1,371 genes or ≈10% of the bee's coding genome. We also detected positive selection associated with the invasion of African-derived honey bees in the New World. We found that introgression of European-derived alleles into Africanized bees was significantly greater for coding than noncoding regions. Our findings demonstrate that Africanized bees exploited the genetic diversity present from preexisting introductions in an adaptive way. Finally, we found a significant negative correlation between FST estimates and the local GC content surrounding coding SNPs, suggesting that AT-rich genes play an important role in adaptive evolution in the honey bee. PMID:18299560

  19. GenColors-based comparative genome databases for small eukaryotic genomes.

    PubMed

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

  20. GenColors-based comparative genome databases for small eukaryotic genomes

    PubMed Central

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. PMID:23193285

  1. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  2. Imaging genomics.

    PubMed

    Hariri, Ahmad R; Weinberger, Daniel R

    2003-01-01

    The recent completion of a working draft of the human genome sequence promises to provide unprecedented opportunities to explore the genetic basis of individual differences in complex behaviours and vulnerability to neuropsychiatric illness. Functional neuroimaging, because of its unique ability to assay information processing at the level of brain within individuals, provides a powerful approach to such functional genomics. Recent fMRI studies have established important physiological links between functional genetic polymorphisms and robust differences in information processing within distinct brain regions and circuits that have been linked to the manifestation of various disease states such as Alzheimer's disease, schizophrenia and anxiety disorders. Importantly, all of these biological relationships have been revealed in relatively small samples of healthy volunteers and in the absence of observable differences at the level of behaviour, underscoring the power of a direct assay of brain physiology like fMRI in exploring the functional impact of genetic variation.

  3. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  4. Ancient genomics.

    PubMed

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  5. Complete mitochondrial genome of the Siamese fighting fish (Betta splendens).

    PubMed

    Song, Ying-Nan; Xiao, Gui-Bao; Li, Jiong-Tang

    2016-11-01

    The Siamese fighting fish (Betta splendens) is one of the popular aquarium fish. Serious attentions have been paid to the biodiversity of the fish. The mitochondrial genome of the Siamese fighting fish is reported to be 17 099 bp and includes 37 genes. The gene organization is similar to other fish mitogenomes. The control region is AT-rich and includes three tandem repeats. Phylogenetic analysis reveals that the fish is close to fish in the Macropodus genus. This mitogenome will assist in studying the mitochondrial variations and population structure in this fish and examine the evolutionary relationship among fish in the Osphronemidae family.

  6. 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

  7. The Structural Genomics Consortium

    PubMed Central

    Jones, Molly Morgan; Castle-Clarke, Sophie; Brooker, Daniel; Nason, Edward; Huzair, Farah; Chataway, Joanna

    2014-01-01

    Abstract The Structural Genomics Consortium (SGC) supports drug discovery efforts through a unique, open access model of public-private collaboration. This study presents the results of an independent evaluation of the Structural Genomics Consortium, conducted by RAND Europe with the Institute on Governance. The evaluation aimed to establish the role of the SGC within the wider drug discovery and PPP landscape, assessing the merits of the SGC open access model relative to alternative models of funding R&D in this space, as well as the key trends and opportunities in the external environment that may impact on the future of the SGC. It also established the incentives and disincentives for investment, strengths and weaknesses of the SGC's model, and the opportunities and threats the SGC will face in the future. This enabled us to assess the most convincing arguments for funding the SGC at present; important trade-offs or limitations that should be addressed in moving towards the next funding phase; and whether funders are anticipating changes either to the SGC or the wider PPP landscape. Finally, we undertook a quantitative analysis to ascertain what judgements can be made about the SGC's past and current performance track record, before unpacking the role of the external environment and particular actors within the SGC in developing scenarios for the future. PMID:28560088

  8. The mitochondrial genome of Baylisascaris procyonis.

    PubMed

    Xie, Yue; Zhang, Zhihe; Niu, Lili; Wang, Qiang; Wang, Chengdong; Lan, Jingchao; Deng, Jiabo; Fu, Yan; Nie, Huaming; Yan, Ning; Yang, Deying; Hao, Guiying; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

    2011-01-01

    Baylisascaris procyonis (Nematoda: Ascaridida), an intestinal nematode of raccoons, is emerging as an important helminthic zoonosis due to serious or fatal larval migrans in animals and humans. Despite its significant veterinary and public health impact, the epidemiology, molecular ecology and population genetics of this parasite remain largely unexplored. Mitochondrial (mt) genomes can provide a foundation for investigations in these areas and assist in the diagnosis and control of B. procyonis. In this study, the first complete mt genome sequence of B. procyonis was determined using a polymerase chain reaction (PCR)-based primer-walking strategy. The circular mt genome (14781 bp) of B. procyonis contained 12 protein-coding, 22 transfer RNA and 2 ribosomal RNA genes congruent with other chromadorean nematodes. Interestingly, the B. procyonis mtDNA featured an extremely long AT-rich region (1375 bp) and a high number of intergenic spacers (17), making it unique compared with other secernentean nematodes characterized to date. Additionally, the entire genome displayed notable levels of AT skew and GC skew. Based on pairwise comparisons and sliding window analysis of mt genes among the available 11 Ascaridida mtDNAs, new primer pairs were designed to amplify specific short fragments of the genes cytb (548 bp fragment) and rrnL (200 bp fragment) in the B. procyonis mtDNA, and tested as possible alternatives to existing mt molecular beacons for Ascaridida. Finally, phylogenetic analysis of mtDNAs provided novel estimates of the interrelationships of Baylisasaris and Ascaridida. The complete mt genome sequence of B. procyonis sequenced here should contribute to molecular diagnostic methods, epidemiological investigations and ecological studies of B. procyonis and other related ascaridoids. The information will be important in refining the phylogenetic relationships within the order Ascaridida and enriching the resource of markers for systematic, population genetic and

  9. The Mitochondrial Genome of Baylisascaris procyonis