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21 results for “single nucleotide polymorphisms (SNPs).”
Single nucleotide polymorphism (SNPs) data for Scurria scurra, Scurria variabilis, Scurria ceciliana and Scurria araucana
<p>The distribution of genetic diversity is often heterogeneous in space, and it usually correlates with environmental transitions or historical processes that affect demography. The coast of Chile encompasses two biogeographic provinces and spans a broad environmental gradient together with oceanographic processes linked to coastal topography that can affect species' genetic diversity. Here, we evaluated the genetic connectivity and historical demography of four <em>Scurria</em> limpets, <em>S. scurra, S. variabilis, S. ceciliana</em> and <em>S. araucana</em>, between ca. 19° S and 53° S in the Chilean coast using genome-wide SNPs markers. Genetic structure varied among species which was evidenced by species-specific breaks together with two shared breaks. One of the shared breaks was located at 22–25° S and was observed in <em>S. araucana</em> and <em>S. variabilis</em>, while the second break around 31–34° S was shared by three <em>Scurria</em> species. Interestingly, the identified genetic breaks are also shared with other low-disperser invertebrates. Demographic histories show bottlenecks in <em>S. scurra</em> and <em>S. araucana</em> populations and recent population expansion in all species. The shared genetic breaks can be linked to oceanographic features acting as soft barriers to dispersal and also to historical climate, evidencing the utility of comparing multiple and sympatric species to understand the influence of a particular seascape on genetic diversity.</p>
Single nucleotide polymorphism (SNPs) data for Scurria scurra, Scurria variabilis, Scurria ceciliana and Scurria araucana
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A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula
<p>This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural <em>Quercus petraea</em> (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.</p>
Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
<p>Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci.</p> <p>We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization.</p> <p>The datasets used to illustrate points in the associated review are provided here together with the R script used to analyse the data. Data are either simulated internal to this script or are SNP data generated as part of other studies and included as compressed binary files readily accessable by reading into R using R base function readRDS(). Refer to the analysis script for examples.</p>
Single Nucleotide Polymorphisms (SNPs) identified from the whole genome sequences of hilsa shad (Tenualosa ilisha) of the Bay of Bengal
<p>The data file contains 792,939 isolated SNPs identified by discoSnp++ v2.3.x (Uricaru et al., 2015) from the whole genome sequence of T. ilisha of the Bay of Bengal. The central sequence of length 2k-1 is seen in upper case, while the flanking sequences are seen in lower case. SNP_higher/lower: one of the two alleles. id: id of the SNP (each SNP has a unique id).</p> <p>FOR SNPs:</p> <p>P_i:pos_Alt1/Alt2: Information about a ith SNP (If more than a unique SNP is found, the following format is used: P_1:pos_Alt1/Alt2,P_2:pos_Alt1/Alt2,...</p> <p>pos: position of the SNP with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.</p> <p>Alt1: One of the two alleles</p> <p>Alt2: the other</p> <p>FOR INDELs:</p> <p>P_1:pos_size_repeatSize</p> <p>pos: predicted position of the indel with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.</p> <p>size: predicted size of the indel</p> <p>repeatSize: Size of the longest sequence both prefix of the indel and prefix of the sequence located just after the insertion.</p> <p>high/low: sequence complexity. If the sequence if of low complexity (e.g. ATATATATATATATAT) this variable would be low</p> <p>nb_pol: number of polymorphism.</p> <p>left_unitig_length: size of the full left extension.</p> <p>right_unitig_length: size of the right extension.</p> <p>left_contig_length: size of the full left extension.</p> <p>right_contig_length: size of the right extension.</p> <p>C1: number of reads mapping the central upper case sequence from the first read set.</p> <p>C2: number of reads mapping the central upper case sequence from the second read set.</p> <p>Q1 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the first read set.</p> <p>Q2 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the second read set.</p> <p>G1: Genotype of the variant in the first read set.</p> <p>G2: Genotype of the variant in the second read set.</p> <p>rank: ranks the predictions according to their read coverage in each condition favoring SNPs that are discriminant between conditions.</p>
Crown morphology in Norway spruce (Picea abies [Karst.] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm
Trees growing at high altitude or latitude have to be adapted, amongst others, to the lower temperatures, a shorter vegetation period, heavier snow load and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day-night shift and seasonal change. Potentially adaptive "candidate" genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation, phenotypic traits measured in natural populations and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterised by superior resistance to snow breakage in regions with heavy snow fall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony) and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.
Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
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Single Nucleotide Polymorphisms (SNPs) data of Metarhizium species for Taxonomic Elucidation of M. anisopliae sensu lato
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Assessing gene flow between Dicranum scoparium Hedw. and D. bonjeanii De Not. (Dicranaceae) using single nucleotide polymorphisms (SNPs)
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Single Nucleotide Polymorphisms (SNPs) Associated With Postoperative Analgesic Failure
ClinicalTrials.gov study NCT03916120. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Three Interacting Single Nucleotide Polymorphisms (SNPs) and the Risk of Preterm Birth in Black Families
ClinicalTrials.gov study NCT00675753. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Association of Single Nucleotide Polymorphisms (SNPs) in Metalloproteinases (MMPs) Genes With the Risk of Primary Knee Osteoarthritis in Greek Population.
ClinicalTrials.gov study NCT04463290. IPD Sharing: YES. Countries: 1. Publications: 25.
Evaluation of Single Nucleotide Polymorphisms (SNPs) in Patients With and Without Diabetic Macular Edema
ClinicalTrials.gov study NCT01168258. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Genetic Association Study Between Single Nucleotide Polymorphisms (SNPs) and Cognitive Performance in Young Bipolar Type I Patients: LICAVALGENE
ClinicalTrials.gov study NCT00969930. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Sperm whale population structure in the eastern and central North Pacific inferred by the use of single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial DNA
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Data from: "454 sequencing of reduced representation libraries to discover single nucleotide polymorphisms (SNPs) in Megabunus harvestmen" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
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Data from: "Identification and assessment of single nucleotide polymorphisms (SNPs) between Culex complex mosquitoes." in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
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Variety differentiation: Development of a powerful CRISPR DETECTR method for the detection of single nucleotide polymorphisms (SNPs)
<p>Supplemental information: Variety differentiation: Development of a powerful CRISPR DETECTR method for the detection of single nucleotide polymorphisms (SNPs). Excel sheets show the raw fluorescence data and calculated sample/NTC and P/N ratios described in the manuscript.</p>
Genomics, Single Nucleotide Polymorphisms (SNPs), and Clinical Neonatology
ClinicalTrials.gov study NCT00315263. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Single Nucleotide Polymorphisms (SNPs) Associated With Postherpetic Neuralgia
ClinicalTrials.gov study NCT03708653. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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International Brain Laboratory public data
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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.