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3,584 results for “genomic analysis”
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion
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Data from: Genome analysis reveals three distinct lineages of the cosmopolitan white shark
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Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae
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Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
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Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture
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Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2
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Supporting code and data to reproduce analysis for: Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms
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Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
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Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis: Summary stats
<p>Summary stats of the genome-wide meta-analysis with METAL software in the article "Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis."</p>
Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination
<p><i>Wolbachia</i> are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced <i>Wolbachia</i> strains in the A, B, C, D, E and F supergroups. Phylogenomic analysis with these core genes indicate that all 33 <i>Wolbachia</i> strains maintain the supergroup relationship classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were discovered in six genes (2.9%) among 210 single copy orthologs. This finding suggests a relatively low frequency of intergroup recombination. Interestingly, they have occurred not only between A and B supergroups (9 events), but also between A and E supergroups (5 events). Maintenance of such transfers suggests possible roles in <i>Wolbachia</i> infection related functions. Comparisons of strain divergence using the five genes of the MLST system show a high correlation (Pearson correlation coefficient r = 0.98) between MLST and whole genome divergences, indicating that MLST is a reliable method for identifying related strains when whole genome data are not available. The phylogenomic analysis and the identified core gene set in our study will serve as a valuable foundation for strain identification and the investigation of recombination and genome evolution in <i>Wolbachia</i>.</p>
Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function
<p>Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3. </p>
Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model
<p>Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using the program PHASE, and random resolution) on estimation of the species tree and evolutionary parameters in analysis of multi-locus genomic data under the MSC model. We found that species tree estimation is robust to phasing errors when species divergences were much older than average coalescent times but may be affected by phasing errors when the species tree is shallow. Estimation of parameters under the MSC model with and without introgression is affected by phasing errors. In particular, random phase resolution causes serious overestimation of population sizes for modern species and biased estimation of cross-species introgression probability. In general the impact of phasing errors is greater when the mutation rate is higher, the data include more samples per species, and the species tree is shallower with recent divergences. Use of phased sequences inferred by the PHASE program produced small biases in parameter estimates. We analyze two real datasets, one of East Asian brown frogs and another of Rocky Mountains chipmunks, to demonstrate that heterozygote phase-resolution strategies have similar impacts on practical data analyses. We suggest that genome sequencing projects should produce unphased diploid genotype sequences if fully phased data are too challenging to generate, and avoid haploid consensus sequences, which have heterozygous sites phased at random. In case the analytical integration algorithm is computationally unfeasible, computational phasing prior to population genomic analyses is an acceptable alternative. </p>
UHGG v1 database for inStrain genome resolved metagenomic analysis
<p>A series of files that are useful for profiling metagenomic communities with the program inStrain.</p>
Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study
<p><span><span>Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic and lifestyle behavioural factors on the risk of T2D, a total of 12,403 individuals were identified as incident T2D cases and a representative sub-cohort of 16,154 individuals was selected from a larger cohort of 340,234 participants with a follow-up time of 3.99 million person-years. We describe the results from a genome-wide association analysis between more than 8.9 million SNPs and T2D risk among 22,326 individuals (9,978 cases and 12,348 non-cases) from the EPIC-InterAct study. The summary statistics to be shared provide a valuable resource to facilitate further investigations into the genetics of T2D. </span></span></p>
Data from: Genomic analysis and prediction within a US public collaborative winter wheat regional testing nursery
The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly-unbalanced datasets common to breeding programs. The Southern Regional Performance Nursery (SRPN) is a public nursery established by the USDA-ARS in 1931 to characterize performance and quality of near-release wheat varieties from breeding programs in the US Central Plains. New entries are submitted annually and can be reentered only once. The trial is grown at more than 30 locations each year and lines are evaluated for grain yield, disease resistance, and agronomic traits. Overall genetic gain is measured across years by including common check cultivars for comparison. We have generated whole-genome profiles via genotyping-by-sequencing for 939 SPRN entries dating back to 1992. We measured the diversity within the nursery and have explored its potential use as a GS training population. GS prediction models across years (average r= 0.33) outperformed year-to-year phenotypic correlation for yield (r=0.27) for a majority of the years evaluated, suggesting that genomic selection has the potential to outperform low heritability selection on yield in these highly variable environments. We also examined the predictability of programs using both program-specific and whole-set training populations. Generally, the predictability of a program was similar with both approaches. These results suggest that wheat breeding programs can collaboratively leverage the immense datasets that are generated from regional testing networks.
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania's Appalachian region
Informed conservation of stream fishes requires detailed understanding of the effects of both natural processes and anthropogenic activities on genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to eastern North America, typically resides in cold, high-quality stream ecosystems. The species has not only faced historical anthropogenic pressures, but also confronts current and future pressures. In a genetic analysis we used a reduced representation sequencing method (ddRADseq) to characterize 63 individuals from 23 streams where Brook Trout are native in the Appalachian region of Pennsylvania. A total of 2,590 loci passed filtering criteria, and 53% displayed significant association with a major stream drainage basin (Susquehanna or Allegheny; mean FST = 0.085). Mapping of the sequencing reads to the Atlantic Salmon Salmo salar genome revealed no clustering of high interdrainage FST values to specific genome regions. Evidence for genetic heterogeneity within each drainage basin was also detected. Stepwise regression of observed heterozygosity against geographic and environmental features revealed that drainage basin and effective area of watersheds were significant predictors of observed heterozygosity of Brook Trout within streams. Natural features such as waterfalls and major drainage basin, as well as the effects of dams and acid-mine drainage have fragmented habitat and shaped genetic diversity within Brook Trout populations in the Appalachian region of Pennsylvania, overall indicating the vulnerability of this species to increased industrialization.
Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree-like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA-BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa.
Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140-kb of orthologous sequence data from colugo museum specimens sampled across their range, and identified large genetic differences between many geographically isolated populations that may result in a 300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Identification and analysis of functional associations among natural eukaryotic genome editing components
<p>The contents of the data files for the manuscript "Identification and analysis of functional associations among natural eukaryotic genome editing components" are described below.</p> <p>Dataset 1 - ies_retention.tab<br> = All IES retention scores used in the manuscript</p> <p>Dataset 2 - oes_retention.tab<br> = OES retention estimates.</p> <p>Supplementary Data S1 - ies_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for all IESs.</p> <p>Supplementary Data S2 - ies_retention_score_correlation_stats_len_le_35bp.txt<br> = Statistics for Spearman's correlations for IESs <= 35 bp.</p> <p>Supplementary Data S3 - ies_retention_score_correlation_stats_len_ge_500bp.txt<br> = Statistics for Spearman's correlations for IESs >= 500 bp.</p> <p>Supplementary Data S4 - oes_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for OESs (>= 300 bp and 3x-70x PGM-KD<br> coverage).</p> <p>Supplementary Data S5 - ies_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all IESs.</p> <p>Supplementary Data S6 - oes_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all OESs.</p> <p>Supplementary Data S7 - ies_vs_oes_retention_score_correlation.comparisons_stats.txt<br> = Statistics for comparisons of the differences in Spearman correlations<br> between IESs and OESs.</p> <p>Supplementary Data S8 - OES.v1.fa<br> = OES sequences.</p> <p> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.