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27 results for “single-nucleotide polymorphism”
Single-nucleotide polymorphisms in isolates Pyricularia oryzae isolates from rice and other hosts
<p>We investigated the presence of inter-lineage hybrids in a set of 886 isolates of the rice-infecting lineage of the rice blast fungus (<em>Pyricularia oryzae</em>).</p> <p>More details in https://doi.org/10.1101/2020.06.02.129296</p> <p>List of files:</p> <p>concatenation_5190SCOs_179isolates.fasta.gz: concatenated sequences of 5190 single copy orthologs from 179 isolates (used in Figures A and B, and computations of polymorphism and divergence in Appendix 1).</p> <p>concatenation_3686SNPs_415isolates.fasta.gz: concatenated polymorphisms identified in 415 isolates at 3686 genomic positions (used in Figure C, Appendix 1).</p> <p>concatenation_503889SNPs_96isolates.fasta.gz: concatenated polymorphisms identified in 96 isolates at 503889 genomic positions (used in Figures D and E, Appendix 1).</p> <p>orthology_table_with_70-15_genemodels.txt: Orthology table, with one orthogroup per line, one species per column, 16445 orthogroups, 179 isolates. The MGG column represents gene models from the 70-15 reference genome MG8, determined subsequently to orthology analysis by blastx of 70-15 sequences against isolate VT0027, which was the closest isolate in a neighbor-net network.</p>
Genotyping-by-sequencing Single-nucleotide Polymorphism Dataset for Corynorhinus rafinesquii (CORA) and Myotis austroriparius (MYAU)
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Genomic population structure of sympatric sexual and asexual populations in a parasitic wasp, Meteorus pulchricornis (Hymenoptera: Braconidae), inferred from six hundred single-nucleotide polymorphism loci
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Fig. 2 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms
Fig. 2. Population tree inferred by TreeMix using all 42 sampling sites across the mountain pine beetle range. Terminal branches are labeled using locality information (see Supp Fig. 1 [online only] for further detail) and migration arrows are colored according to migration weight.
Fig. 3. Scenario 9 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms
Fig. 3. Scenario 9 was identified as the 'best' from 11 competing phylogeographic scenarios. This scenario represents an east-to-west colonization route with stable population sizes in which cluster 4 is derived from clusters 1 and 3 through admixture. Terminal branch labels are consistent with the five STRUCTURE clusters identified (Fig. 1). T = time expressed as number of generations assuming one generation per year; R = inferred migration rate.
Fig. 1 in Inferring Ancestry and Divergence Events in a Forest Pest Using Low-Density Single-Nucleotide Polymorphisms
Fig. 1. Map of mountain pine beetle sites throughout western North America. Each site is represented by a pie chart depicting the average assignment (Q values) of individuals to one of five STRUCTURE clusters (K = 5).
Data from: Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks
An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5112 contigs (6542 putative in silico SNPs). The 7913 SNPs were genotyped across the six parental individuals, full-sib progenies (one within each species and two interspecific crosses between Q. petraea and Q. robur) and three natural populations from south-western France that included two additional interfertile white oak species (Q. pubescens and Q. pyrenaica). The genotyping success rate in mapping populations was 80.4% overall and 72.4% for polymorphic SNPs. In natural populations, these figures were lower (54.8% and 51.9%, respectively). Illumina genotype clusters with compression (shift of clusters on the normalized x-axis) were detected in ~25% of the successfully genotyped SNPs and may be due to the presence of paralogues. Compressed clusters were significantly more frequent for SNPs showing a priori incorrect Illumina genotypes, suggesting that they should be considered with caution or discarded. Altogether, these results show a high experimental error rate for the Infinium array (between 15% and 20% of SNPs potentially unreliable and 10% when excluding all compressed clusters), and recommendations are proposed when applying this type of high-throughput technique. Finally, results on diversity levels and shared polymorphisms across targeted white oaks and more distant species of the Quercus genus are discussed, and perspectives for future comparative studies are proposed.
The Expression of Immune Checkpoint CD28 rs1980422-related Single-nucleotide Polymorphisms in the Primary Immune Thrombocytopenia
ClinicalTrials.gov study NCT05468866. IPD Sharing: YES. Countries: 1. Publications: 4.
" Effect of Single-nucleotide Polymorphism of CD40 Gene rs1883832 C/T on the Risk of Immune Thrombocytopenic Purpura "
ClinicalTrials.gov study NCT05585944. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Data from: A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples
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Data from: Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct
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Data from: Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks
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Data from: Predictions of single-nucleotide polymorphism differentiation between two populations in terms of mutual information
Mutual information (I) provides a robust measure of genetic differentiation for the purposes of estimating dispersal between populations. At present, however, there is little predictive theory for I. The growing importance in population biology of analyses of single-nucleotide and other single feature polymorphisms (SFPs) is a potent reason for developing an analytic theory for I with respect to a single locus. This study represents a first step towards such a theory. We present theoretical predictions of I between two populations with respect to a single haploid biallelic locus. Dynamical and steady-state forecasts of I are derived from a Wright-Fisher model with symmetric mutation between alleles and symmetric dispersal between populations. Analytical predictions of a simple Taylor approximation to I are in good agreement with numerical simulations of I and with data on I from SFP analyses of dispersal experiments on Drosophila fly populations. The theory presented here also provides a basis for the future inclusion of selection effects and extension to multi-allelic loci.
Data from: Characterization of the gray whale Eschrichtius robustus genome and a genotyping array based on single-nucleotide polymorphisms in candidate genes
Genetic and genomic approaches have much to offer in terms of ecology, evolution, and conservation. To better understand the biology of the gray whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome and produced an assembly that contains ∼95% of the genes known to be highly conserved among eukaryotes. From this assembly, we annotated 22,711 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs). Using this assembly, we generated a curated list of candidate genes potentially subject to strong natural selection, including genes associated with osmoregulation, oxygen binding and delivery, and other aspects of marine life. From these candidate genes, we queried 92 autosomal protein-coding markers with a panel of 96 SNPs that also included 2 sexing and 2 mitochondrial markers. Genotyping error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed heterozygosity was 0.33 averaged over all autosomal markers. This level of variability provides substantial discriminatory power across loci (mean probability of identity of 1.6 × 10−25 and mean probability of exclusion >0.999 with neither parent known), indicating that these markers provide a powerful means to assess parentage and relatedness in gray whales. We found 29 unique multilocus genotypes represented among our 36 biopsies (indicating that we inadvertently sampled 7 whales twice). In total, we compiled an individual data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray whale (EGW). The lone EGW we sampled was no more or less related to the WGWs than expected by chance alone. The gray whale genomes reported here will enable comparative studies of natural selection in cetaceans, and the SNP markers should be highly informative for future studies of gray whale evolution, population structure, demography, and relatedness.
Data from: Predictions of single-nucleotide polymorphism differentiation between two populations in terms of mutual information
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Data from: Characterization of the gray whale Eschrichtius robustus genome and a genotyping array based on single-nucleotide polymorphisms in candidate genes
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Intracranial aneurysm associated single-nucleotide polymorphisms alter regulatory DNA in the human circle of Willis
GEO Series GSE107196. Homo sapiens. 14 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression
GEO Series GSE15675. Mus musculus. 12 samples. Type: Other.
Genome-wide analysis of esopageal adenocarcinoma tumor biopsy using high-density single-nucleotide polymorphism arrays.
GEO Series GSE10506. Homo sapiens. 24 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)
Recent advances in high-throughput sequencing technologies have offered the possibility to generate genome-wide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters, and to evaluate potential adaptive divergence. Here, we identified 27 556 single-nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation was identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP dataset of top quality score per contig or neutral loci. However, the two analyzed populations were highly differentiated based on SNP dataset of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST-based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. BLAST2GO annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant BLASTX matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in the present study provided a valuable tool for future population genetics and genomics studies of L. polyactis.
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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.