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15,277 results for “GENETICS”
Figure 3 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 3. Prevalence of three different alleles of Pvmsp-3β (A, B, C) from PCR-RFLP.
Data and appendices: Genetic structure of the European white elm (Ulmus laevis Pall., Ulmaceae) in Switzerland
<p>This dataset is linked to the following article published in Annals of Forest Science: Dermelj, L., Fragnière, Y., Jacob, G. et al. Genetic structure of the European white elm (Ulmus laevis Pall., Ulmaceae) in Switzerland. Annals of Forest Science 81, 28 (2024). <a href="https://urldefense.com/v3/__https://doi.org/10.1186/s13595-024-01245-8__;!!Dc8iu7o!yKfGPXx0qHn-nE984OtuCUPPKaVjkUX03CZMhD3un5K_DjKgv8OrJB1nXYJdoWBTDKXDNA196eOKhBbjLjqqPgOm$" target="_blank" rel="noopener noreferrer">https://urldefense.com/v3/__https://doi.org/10.1186/s13595-024-01245-8__;!!Dc8iu7o!yKfGPXx0qHn-nE984OtuCUPPKaVjkUX03CZMhD3un5K_DjKgv8OrJB1nXYJdoWBTDKXDNA196eOKhBbjLjqqPgOm$</a></p> <p> </p> <pre> </pre>
Fig. 1 in Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa)
Fig. 1 Th_ origin (N = 92) of Paramecium biaurelia strains us_d in pr_s_nt studi_s
Genotyping measures and population genetic indices for assesing reproductive modes of polyploid Ludwigia grandiflora subsp. hexapetala in western Europe
<p>Raw data used to assess reproductive modes in 53 sampled populations in western Europe (France and northern Spain).</p> <p><em>Ludwigia grandiflora </em>subsp.<em> hexapetala</em> (<em>Lgh</em>) is a hermaphrodite, polyploid, partially clonal and heteromorphic plant that recently colonized multiple countries worldwide. Individuals in this species are either self-incompatible caused by a late-acting self-incompatible (LSI) system developing long-styled flowers, or self-compatible (SC) developing short-styled flowers. We used a SNP approach allowing confident allele dosage to genotype 53 LSI and SC populations of <em>Lgh</em> in France and northern Spain. We measured their genetic diversity and assessed their reproductive modes using methods adapted to autopolyploid species. </p>
Fig. 3 in Evaluation of field dispersal and survival capacity of the genetic sexing strain Tapachula-7 of Anastrepha ludens (Diptera: Tephritidae)
Fig. 3. Survival of SMR and Tap-7 strains of Anastrepha ludens afer aerial release.
Supplementary Materials for Respiratory Syncytial Virus Genetic Diversity and Lineage Changes in Ireland pre- and post-COVID-19 pandemic
<p><span>The datasets presented here are the list of publicly available reference sequences used in NextClade (</span><a href="https://github.com/rsv-lineages"><span>https://github.com/rsv-lineages</span></a><span>) to provide the lineage classification of samples and used as reference for analysis of Irish RSV sequences (Supplementary Table 1), the list of sequenced Human respiratory syncytial viruses (RSV) in the Republic of Ireland during the period 2015-2024 (Supplementary Table 2) and the details of sequences downloaded from GISAID corresponding to European RSV sequences for the same period of time.</span></p> <p><span> </span></p> <p><span>Description of the data and file structure</span></p> <p><span>The files in this dataset were formatted in Microsoft Excel 2019 to allow easy access and manipulation of the data. The data corresponds to details on the sequences used in the analysis of RSV in Europe during the 2015-2024 period. The contents of the files are described below: -<strong>Supplementary Table 1</strong>: NextClade Reference Sequences publicly available at </span><a href="https://github.com/rsv-lineages"><span>https://github.com/rsv-lineages</span></a><span>. -<strong>Supplementary Table 2</strong>: Irish RSV Sequence Details contains details on the sequences generated in our study with the GenBank accession number, the GISAID accession number, reported collection RSV season, Nextclade assigned taxonomical clade. -<strong><span>Supplementary Table 3</span></strong>: European RSV Sequence Details contains a list of European RSV sequences downloaded from GISAID (</span><a href="https://gisaid.org/"><span>https://gisaid.org/</span></a><span>) with details on the sampling RSV season, the accession number, country of collection, and lineage assigned by NextClade.</span></p> <p><span> </span></p> <p><span>Sharing/Access information</span></p> <p><span>The databases used to extract and deposit the data were:</span></p> <p><span>-GenBank: the North American repository of sequences and publicly available at: </span><a href="https://www.ncbi.nlm.nih.gov/genbank/"><strong><span>https://www.ncbi.nlm.nih.gov/genbank/</span></strong></a><span> </span></p> <p><span>-GISAID:International consortium of sequences with some metadata and clinical data. It is a semi-public repository with easy access requiring only to create an account. Available at: </span><a href="https://gisaid.org/"><strong><span>https://gisaid.org/</span></strong></a></p> <p><span>-Github: reference sequences of RSV are available at the repository </span><a href="https://github.com/"><strong><span>https://github.com/</span></strong></a></p>
Genetics of Cardiac Aging Implicate Organ-Specific Variation - GWAS Summary Stats and Model Weights
Open the record for dataset details and reuse information.
Figure 3 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations
Figure 3. Results of AMOVA analysis among and within the studied populations.
Fig. 1 in Soluble proteins in Messor structor (Latreille, 1798) (Hymenoptera: Formicidae) populations from Bulgaria - genetic variability and possible usage as population-genetic markers
Fig. 1. Sampling locations.
Fig. 1 in Trypanosomes genetic diversity, polyparasitism and the population decline of the critically endangered Australian marsupial, the brush tailed bettong or woylie (Bettongia penicillata)
Fig. 1. Geographical origin of the different species of marsupials trapped in this study.
Fig. 1 in Marked genetic diversity within Blastocystis in Australian wildlife revealed using a next generation sequencing-phylogenetic approach
Fig. 1. Map showing Melbourne's water catchment areas where samples were collected (2009-2022).
Fig. 5 in Phylogeography and Genetic Structure of the Bush Cricket (Orthoptera, Tettigoniidae) in Southern China.
Fig. 5. Divergence time estimation based on combined mitochondrial data of D. fissa.
Fig. 1 in Phylogeography and Genetic Structure of the Bush Cricket (Orthoptera, Tettigoniidae) in Southern China.
Fig. 1. The geographic distribution collection points.
Fig. 8 in Phylogeography and Genetic Structure of the Bush Cricket (Orthoptera, Tettigoniidae) in Southern China.
Fig. 8. The result of the BBM with RASP
ZymoSoups: A high-throughput forward genetics method for rapid identification of virulence genes in Zymoseptoria tritici
<p>These data were used to generate figures and summarise the number of mutations in 18 re-sequenced genomes of <em>Zymoseptoria tritici. </em>The isolates genotyped in this VCF file are all UV-mutegenized strains of the reference isolate IPO323.</p> <p><strong>Abstract</strong></p> <p><span><span>Septoria tritici blotch is caused by the fungus </span></span><em><span><span>Zymoseptoria</span><span> tritici</span> </span></em><span><span>and</span><span> poses a major threat to wheat </span><span>productivity</span><span>. </span><span>There are over twenty mapped loci in wheat that confer strong (gene-for-gene) resistance </span><span>against this pathogen</span><span>, h</span><span>owever</span> <span>t</span><span>he corresponding genes in </span></span><em><span><span>Z. tritici</span></span></em><span><span> that confer virulence against distinct </span></span><span><span>R</span></span><span> <span>genes </span><span>remain</span> <span>largely unknown</span><span>. </span><span>In this study, we developed a</span> <span>rapid </span><span>forward genetics </span><span>methodology</span> <span>to </span><span>identify</span><span> genes that enable </span></span><em><span><span>Z. tritici</span></span></em><span><span> to gain virulence </span><span>on </span><span>previously resistant wheat varieties. </span><span>We</span><span> used the known</span><span> gene-for-gene interaction between </span></span><span><span>Stb6</span></span><span><span> and </span></span><span><span>AvrStb6</span></span><span><span> as </span><span>a </span><span>proof of concept that this method could quickly recover single candidat</span><span>e</span><span> virulence genes</span><span>. We subjected the avirulent </span></span><em><span><span>Z. tritici</span></span></em><span><span><em> </em>strain IPO323</span><span>, which carries the recogni</span><span>z</span><span>ed </span></span><span><span>AvrStb6</span></span><span><span> allele,</span><span> to UV mutagenesis</span><span> and</span><span> generat</span><span>ed</span><span> a library of over </span><span>66</span><span>,</span><span>000 </span><span>surviving spores</span><span>. </span><span>We screen</span><span>ed</span><span> these </span><span>survivors</span><span> on leaves of the resistant wheat variety Cadenza</span><span>,</span><span> in</span><span> mixtures</span> <span>(</span><span>soups</span><span>)</span><span> ranging from </span><span>100</span><span>-</span><span>500</span> <span>survivors</span><span> per soup. </span><span>We </span><span>identified</span><span> five soups</span><span> with </span><span>a </span><span>gain</span><span>-</span><span>of</span><span>-</span><span>virulence (</span><span>GoV</span><span>)</span><span> phenotype </span><span>relative</span><span> to the IPO323 parental strain</span><span> and re-sequenced 18 individual isolates, including four control isolates and two </span><span>isolates</span><span> lacking virulence</span><span>,</span><span> when screened </span><span>individually.</span> <span>Of </span><span>the </span><span>12 </span><span>confirmed </span><span>GoV</span> <span>isolates</span><span>, o</span><span>ne had a single nucleotide polymorphism (SNP) in the </span></span><span><span>AvrStb6</span></span><span><span> coding region. </span><span>T</span><span>he other 11 </span><span>GoV</span> <span>isolates</span> <span>exhibited</span> <span>large</span><span> (~70Kb)</span> <span>deletions at the end of chromosome 5, including the </span></span><span><span>AvrStb6</span></span><span><span> locus. </span><span>Our findings </span><span>demonstrate</span><span> the </span><span>efficiency </span><span>of this forward genetic approach in elucidating the genetic basis of qualitative resistance to </span></span><span><span>Z. tritici</span></span><span><span> and the </span><span>potential </span><span>to rapidly </span><span>identify</span><span> other</span><span>,</span><span> currently unknown</span><span>,</span> </span><span><span>Avr</span></span><span><span> genes in this pathogen. </span></span></p> <p><span><strong>Analysis pipeline</strong></span></p> <p><span>The pipeline used to generate this filtered vcf file and tab delimited file is publicly available at https://github.com/megancamilla/GATK4_Zymoseptoria</span></p> <p><span><strong>Isolate Data Accessibility</strong></span></p> <p><span><span>The individual fastq files for each isolate included in this study have been uploaded to NCBI's Short Read Archive (SRA), project number PRJNA1017776. This project </span><span>contains</span><span> 18 re-sequenced samples (SAMN37407989-SAMN37407972),</span> <span>which are UV mutagenized IPO323. Short Read Archive (SRA) accession numbers are SRR26072101-SRR26072118. </span> </span></p>
Identifying genetic variants associated with chromatin looping and genome function
<p><span>Here<span> we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30 donors and identify QTLs that associate with genotype-dependent and/or allele-specific variation of HiChIP contacts defining loops between active regulatory regions (iQTLs). We observe a substantial overlap between iQTLs and previously defined eQTLs and histone QTLs, and an enrichment for fine-mapped QTLs and GWAS variants. Furthermore, we describe a distinct subset of nCD4 iQTLs, for which the significant variation of chromatin contacts in nCD4 are translated into significant eQTL trends in CD4 T cell memory subsets. Finally, we define connectivity-QTLs as iQTLs that are significantly associated with concordant genotype-dependent changes in chromatin contacts over a broad genomic region (e.g., GWAS SNP in the <em>RNASET2</em> locus). Our results demonstrate the importance of chromatin contacts as a complementary modality for QTL mapping and their power in identifying novel classes of QTLs linked to cell-specific gene expression and connectivity.</span></span></p> <p> </p> <p><span><span>This repository contains the source code, supplementary datasets for the manuscript (Nature Communications 2024).</span></span></p>
Fig. 1 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 1. Plastid genomic map of Aster altaicus var. uchiyamae.
Fig. 1 in Testing microsatellite loci and preliminary genetic study for Eurasian otter in South Korea
Fig. 1. Spraints collection sites along Ungokcheon Stream, Bonghwa-gun, Gyeongsangbuk-do.
Fig. 1 in Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode
Fig. 1. Plastid genomic map of Dendranthema sp. K247003.
Fig. 2. A in A preliminary study of genetic structure and relatedness analysis of Nutria (Myocastor coypus) in Upo Wetland
Fig. 2. A bar plot representing the estimated membership coefficients of nutria individuals (K=2).
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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.