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294 results for “SNPs”
all SNPs and genes assigned to each LD block
<p><strong>Downloadable data files</strong></p> <p>The DistiLD resource integrates information on:</p> <ul> <li>Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS)</li> <li>Links between SNPs and genes based on linkage disequilibrium (LD) data from <a href="http://www.hapmap.org/">HapMap</a></li> </ul> <p>...</p> <p> </p> <p>The second file contains <a href="http://distild.jensenlab.org/lds.tsv.gz">all SNPs and genes assigned to each LD block</a> [114MB] in the following format:</p> <ol> <li>Linkage disequilibrium (LD) block</li> <li>Reference SNP (rs) number of SNPs in LD block</li> <li>Ensembl genes in LD block</li> </ol>
Whole-Genome Resequencing identifies SNPs in Sucrose Synthase and Sugar Transporter Genes Associated with Sweetness in Coconut
<p><span>This vcf file constitute underlying raw data material for the manuscript</span> "<span>Whole-Genome Resequencing identifies SNPs in Sucrose Synthase and Sugar Transporter Genes Associated with Sweetness in Coconut"</span>. <span>The SNP genotype data came from a whole-genome resequencing and were called using an unpublished coconut reference genome. SNPs with a non-missing and minor allele frequency (MAF) less than 5% were removed. Finally, 19,149,289 SNPs were selected and used in the population study and gene mining.</span></p>
group-5-NF alignment and SNPs
<p>Alignment of reads for the BSA bulk 'non-flowering' (NF) against the <em>B. oleracea</em> reference genome (as BAM file), and subsequent SNP calling results (as compressed VCF file).</p> <p> </p>
group-3-LF alignment and SNPs
<p>Alignment of reads for the BSA bulk 'late flowering' (LF) against the <em>B. oleracea</em> reference genome (as BAM file), and subsequent SNP calling results (as compressed VCF file).</p>
group-2-IF alignment and SNPs
<p>Alignment of reads for the BSA bulk 'intermediate flowering' (IF) against the <em>B. oleracea</em> reference genome (as BAM file), and subsequent SNP calling results (as compressed VCF file).</p> <p> </p>
237 rice cultivar genotype dataset with 91,800 SNPs
<p>This repository contains a genotype dataset for Shimono et al. 2022.</p> <p>DOI: https://doi.org/10.21203/rs.3.rs-1544941/v2</p> <p> </p>
Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs
<p><em>Lupinus mutabilis</em> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (F<sub>st</sub>) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative F<sub>is</sub> for both populations, demonstrating that, like other <em>Lupinus</em> species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.</p>
Data for: SNPs detected in pool-seq data from resistant and susceptible Cimex lectularius populations
<p>In the last few years, the bed bug <em>Cimex lectularius</em> has been an increasing problem world-wide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in <em>Cimex lectularius</em>, we compared the genetic composition of two recent and resistant populations with that of two ancientsusceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes, andwas also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitute a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.</p>
American Crow SNPs and microsatellite data
<p>Infectious diseases can cause steep declines in wildlife populations, leading to changes in genetic diversity that may affect the susceptibility of individuals to infection and the overall resilience of populations to pathogen outbreaks. Here, we examine evidence for a genetic bottleneck in a population of American crows (<em>Corvus</em> <em>brachyrhynchos</em>) before and after the emergence of West Nile virus (WNV). More than 50% of marked birds in this population were lost over the two-year period of the epizootic, representing a 10-fold increase in adult mortality. Using analyses of SNPs and microsatellite markers, we tested for evidence of a genetic bottleneck and compared levels of inbreeding and immigration in the pre- and post-WNV populations. Counter to expectations, genetic diversity (allelic diversity and the number of new alleles) increased after WNV emergence. This was likely due to increases in immigration, as the estimated membership coefficients were lower in the post-WNV population. Simultaneously, however, the frequency of inbreeding appeared to increase: mean inbreeding coefficients were higher among SNP markers, and heterozygosity-heterozygosity correlations were stronger among microsatellite markers, in the post-WNV population. These results indicate that loss of genetic diversity at the population level is not an inevitable consequence of a population decline, particularly in the presence of gene flow. The changes observed in post-WNV crows could have very different implications for their response to future pathogen risks, potentially making the population as a whole more resilient to a changing pathogen community, while increasing the frequency of inbred individuals with elevated susceptibility to disease.</p>
Prunus armeniaca SNPs dataset
<p>-"armeniaca.SNPs.vcf.gz": dataset including SNPs genotypes for 255 individuals of <em>Prunus armeniaca</em> from Central Asia, filtered from Groppi et al. 2021 (https://www.nature.com/articles/s41467-021-24283-6). </p> <p>-"P.armeniaca Q-values.xlsx": fastStructure Q-value assignment as obtained in Groppi et al. (2021) for each individual (indicated by unique labels in the first column). Q-value assignments to the two main Asian gene pools ("Northern" and "Southern" gene pools).</p> <p>This dataset was prepared in association with the manuscript:</p> <p>Gargiulo R., Decroocq V., González-Martínez S.C., Paz-Vinas I., Aury J-M., Lesur Kupin I., Plomion C., Schmitt S., Scotti I., Heuertz M. 2023. Estimation of contemporary effective population size in plant populations: limitations of genomic datasets. bioRxiv 2023.07.18.549323; doi: https://doi.org/10.1101/2023.07.18.549323</p> <p>See the analytical workflow at: https://github.com/Ralpina/Ne-plant-genomic-datasets/blob/main/README.md (https://doi.org/10.5281/zenodo.8134169)</p> <p> </p>
Hetaerina SNPs data for: Genomic differentiation and niche divergence in the Hetaerina americana (Odonata) cryptic species complex
<p class="MsoNormalCxSpFirst"><span>The evolution of reproductive barriers, that is, the speciation process, implies the limitation of gene flow between populations. Different patterns of genomic differentiation throughout the speciation continuum may provide insights into the causal evolutionary forces of species divergence. In this study, we analyzed a cryptic species complex of the genus <em>Hetaerina</em> (Odonata). This complex includes <em>H. americana</em> and <em>H. calverti</em>; however, in <em>H. americana</em>, two highly differentiated genetic groups have been previously detected, which, we hypothesize, may correspond to different species with low morphological variation. We obtained single nucleotide polymorphism (SNP) data for 90 individuals belonging to the different taxa in the complex and carried out differentiation tests to identify genetic isolation. The results from STRUCTURE and discriminant analysis of principal components (DAPC), based on almost 5,000 SNPs, confirmed the presence of three highly differentiated taxa. Also, we found <em>F</em><sub>ST </sub>values above 0.5 in pairwise comparisons, which indicates a considerable degree of genetic isolation among the suggested species. We also found </span><span>low climatic niche overlap among all taxa, suggesting that each group occurs at specific conditions of temperature, precipitation and elevation</span><span>. We propose that <em>H. americana</em> comprises two cryptic species, which may be reproductively isolated by ecological barriers related to niche divergence, since the morphological variation is minimal and, therefore, mechanical barriers are probably less effective compared to other related species such as <em>H. calverti</em>.</span></p>
Data from: SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)
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De novo assembly of SNPs in VCF format for 112 individualss of Campylorhynchus in western Ecuador
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Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
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Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
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High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)
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American Crow SNPs and microsatellite data
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Data for: SNPs detected in pool-seq data from resistant and susceptible Cimex lectularius populations
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Genotypes and geographic positions of 5797 European white oaks from 636 locations genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria
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The application of short and highly polymorphic microhaplotypes based on nonbinary-SNPs in kinship testing of extremely degraded samples
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Allen Brain Atlas
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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.