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2,785 results for “genotypes”
Liftover of DGRP D.melanogaster genotypes to reference genome assembly v6.0, with QC graph
<p>Output are vcf and plink-format genotype files. Also provided are the run code in bash and R, the logs, summary statistics, and a graph showing how the positions of SNPs have changed.</p>
Individual multilocus genotypes from four populations of Helichrysum arenarium (Asteraceae) from Belgium and Germany
<p>Individual multilocus genotypes based on 11 microsatellites loci from four populations of <em>Helichrysum arenarium</em> (Asteraceae) from Belgium and Germany. For more details, see Van Rossum et al. 2024 "Genetic diversity assessment of <em>Helichrysum arenarium</em> (Asteraceae) for the genetic restoration of declining populations" in Ecology and Evolution</p>
Variation in personality shaped by evolutionary history, genotype, and developmental plasticity in response to feeding modalities in the Arctic charr
<p>Animal personality has been shown to be influenced by both genetic and environmental factors and shaped by natural selection. Currently, little is known about mechanisms influencing the development of personality traits. This study examines the extent to which personality development is genetically influenced and/or environmentally responsive (plastic). We also investigated the role of evolutionary history, assessing whether personality traits could be canalized along a genetic and ecological divergence gradient. We tested the plastic potential of boldness in juveniles of five Icelandic Arctic charr morphs (<em>Salvelinus</em> <em>alpinus</em>), including two pairs of sympatric morphs, displaying various degrees of genetic and ecological divergence from the ancestral anadromous charr, split between treatments mimicking benthic vs. pelagic feeding modalities. We show that differences in mean boldness are mostly affected by genetics. While the benthic treatment led to bolder individuals overall, the environmental effect was rather weak, suggesting that boldness lies under strong genetic influence with reduced plastic potential. Finally, we found hints of differences by morphs in boldness canalization through reduced variance and plasticity, and higher consistency in boldness within morphs. These findings provide new insights into how behavioural development may impact adaptive diversification.</p>
Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance
<p>Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (<em>Acidovorax radicis</em>) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (<em>Hordeum vulgare</em>). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without <em>A. radicis</em>. Results showed that across all plant varieties <em>A. radicis</em> increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while <em>A. radicis</em> inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of <em>A. radicis</em>, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.</p>
Fig. 2 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 2. Genotyping of Cryptosporidium spp. in strawcolored fruit bats by small subunit rRNA-based PCRRFLP. Upper panel: SspI RFLP patterns; lower panel: VspI RFLP patterns; M: 100-bp molecular markers; H: C. hominis positive control; P: C. parvum positive control; B1: Cryptosporidium bat genotype XIV; B2: Cryptosporidium bat genotype XV.
Fig. 4 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 4. Phylogeny of Enterocytozoon bieneusi genotypes in bats based on Bayesian inference analysis of sequences of the internal transcribed spacer of the rRNA gene. The posterior probability values are indicated on the branches. Red ones are E. bieneusi genotypes identified in straw-colored fruit bats in the present study. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
SNPs genotypes of southern beech Nothofagus dombeyi
<p>Geogenomics seeks to understand geological processes linked to lineage divergence. However, the mechanisms that conserve ancient signals despite gene flow are still unclear. In the southern beech, the deep lineage divergence produced by vicariant events is associated with ancient marine transgressions. We hereby evaluate the hypothesis that this divergence is maintained by diversifying selection. The lineage divergence using AMOVA, principal coordinate analysis, assignment tests, and multiple matrix regression analyses was assessed using chloroplast DNA and neutral and outlier SNPs. Several environmental variables were used to characterize potential within-species niche structuring and genotype-environment associations. Two deep-rooted latitudinally structured lineages resulted from cpDNA, the northern cluster being more genetically diverse than the southern one. Of the total of 2,943 SNPs, 33 were identified as outliers and produced two genetic clusters. Neutral SNPs yielded no structure by AMOVA, whereas higher (>75%) <em>F</em><sub>st</sub> values were obtained for cpDNA and outlier SNPs. Precipitation variables were mostly associated with population clusters and suggested two climatic niches, consisting of cold and dry in the south and more variable precipitation, temperature, and soil conditions in the north. Associations of genetic distance with environment and geography suggested IBD and IBE effects. Ancient lineage divergence in <em>N. dombeyi,</em> originally driven by vicariance, has been maintained by diversifying selection under distinct environmental conditions that also define distinct within-species niches. Deeply rooted phylogeographic breaks can be conserved in continuously distributed species in the absence of current geographic barriers. Yet physical gradients exert differential selective pressures, which are maintained in the face of potential gene flow. As a result, selection can lead to geographically localized and differentially adapted groups of populations that can be detected by a combination of traditional phylogeographic and novel genomic methods.</p>
Genotypes for ancient Baltic sheep
<p>Pseudohaploid genotype calls for five ancient sheep genomes from the Baltic Sea region.</p> <p>WGS -- SNP calls at polymorphic sites ascertained from WGS data of wild sheep relatives, coordinates correspond to Oar4.0.</p> <p>SNPCHP -- SNP calls at polymorphic sites from the Illumina Ovine Infinium® HD 600K chip, coordinates correspond to Oar3.1</p> <p>Description on data preparation and genotype calling can be found in our article.</p> <p> </p>
Effective seed sterilization methods require optimization across maize genotypes
<p>Studies of plant-microbe interactions using synthetic microbial communities (SynComs) often require the removal of seed-associated microbes by seed sterilization before inoculation to provide gnotobiotic growth conditions. A diversity of seed sterilization protocols have been developed in the past and have been used on different plant species with various amounts of validation. From these studies, it has become clear that each plant species requires its own optimized sterilization protocol. It has, however, so far not been tested if the same protocol works equally well for different varieties and seed sources of one plant species. We evaluated six seed sterilization protocols on two different varieties (Sugar Bun & B73) of maize. All unsterilized maize seeds showed fungal growth upon germination on filter paper, highlighting the need for a sterilization protocol. A short sterilization protocol with hypochlorite and ethanol was sufficient to prevent fungal growth on Sugar Bun germinants, however, a longer protocol with heat treatment and germination in fungicide was needed to obtain clean B73 germinants. This difference may have arisen from the effect of either genotype or seed source. We then tested the protocol that performed best for B73 on three additional maize genotypes from four sources. Seed germination rates and fungal contamination levels varied widely by genotype and geographic source of seeds. Our study shows that consideration of both variety and seed source is important when optimizing sterilization protocols and highlights the importance of including seed source information in plant-microbe interaction studies that use sterilized seeds.</p>
Responsiveness of the broad bean weevil Bruchus rufimanus Boh. to different Vicia faba L. genotypes
<p><span>The broad bean weevil <em>Bruchus rufimanus</em> Boh., also called bruchid beetle, is a major pest of Vicia faba L. given that larvae develop inside the seeds causing direct quality losses in agricultural products. Recurrent chemical applications are inappropriate because they represent a serious threat to pollinators in general. In addition, biological control approaches that have been attempted so far showed limited effectiveness, which makes studies of methods to control bruchid populations extremely important. Breeding resistant cultivars is the most adequate approach to achieve efficient levels of pest resistance and promote sustainable agriculture. To explore the mechanisms underlying bruchid resistance, we explored B. rufimanus behavior in different life stages and plant preference in feeding, oviposition and larval survival into adulthood both in greenhouse experiments and in the field. Our greenhouse results showed that females, compared to males, have preferences for flowers from some genotypes over the others although the choices made did not correspond with the laying preference. The egg laying preference of females was significantly affected by cultivars. This attraction could be explained by the number of seeds per pod produced by the genotypes, while in the field flowering time influenced bruchid infestation. Moreover, the survival of the larva into adulthood was greater in certain genotypes over the others. The results of our study lay the groundwork for further analyses to finely dissect V. faba resistance towards bruchids and pave the way for the development of methods to predict potential resistant genotypes in research and breeding programs.</span></p>
Genotyping and phenotyping data for Genome-wide analyses of body fat reserves in ewes
<p><strong>Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for livestock sustainability, allowing animals to cope with more variable environments. BRD has previously been reported to be heritable in ruminants. In the present study, we conducted genome-wide studies (GWAS) in sheep to determine genetic variants associated with BRD. BR levels and BR changes over time were obtained through body condition score measurements at eight physiological stages throughout each productive cycle in Romane ewes (n=1034) and were used as phenotypes for GWAS. After quality controls and imputation, 48,513 single nucleotide polymorphisms (SNP) were included in the GWAS. Among the QTLs identified, a major QTL associated with BR levels during pregnancy and lactation was identified on chromosome 1. In this region, several significant SNPs mapped to the leptin receptor gene (LEPR), among which one SNP mapped to the coding sequence. The point mutation induces the p.P1019S substitution in the cytoplasmic domain, close to tyrosine phosphorylation sites. The frequency of the SNP associated with increased BR levels was 32%, and the LEPR genotype explained up to 5% of the variance of the trait. These results provide strong evidence for involvement of LEPR in the regulation of BRD in sheep and highlight it as a major candidate for improving adaptive capacities.</strong></p>
Morphological and physiological characteristics of cassava genotypes on dry-land of ultisol soil in Indonesia
<p>This data showed the characterization of morphological and physiological characters of some cassava genotypes in Indonesia that were collected from some areas in Indonesia and now, planting in the IPB Germplasm Farm Collection at Bogor Regency, Indonesia. We have more than 50 genotypes collections. </p>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: discovery cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the discovery cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include: </p> <p>(1) a file mapping the SNP data subject IDs to the TCR repertoire data subject IDs (gwas_id_mapping.tsv)<br> (2) a file including the PCAir PCs, self-reported ancestry, and genomic ancestry for each subject (all_pc_air.txt)<br> (3) a file including the PCAir variance explained by each PC (all_pc_air_variance.txt)<br> (3) a file including the SNP ID, chromosome, hg19 position, allele, rsid, and quality control metrics for each SNP in the SNP array (emerson_snp_rs_data.tsv)<br> (4) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (5) a file including predicted TRBD2 allele genotypes for each subject (emerson_trbd2_alleles.tsv)<br> (6) Parsed TCRB repertoire data. These raw data were first published in Emerson et. al, <em>Nature Genetics </em>2017. (emerson_parsed_tcrb.tgz)</p> <p><strong>Corresponding discovery cohort raw TCR repertoire data is available here: </strong>https: //doi.org/10.21417/B7001Z (ImmuneACCESS database)<br> <strong>Corresponding discovery cohort SNP data is available here:</strong> https: //www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001918.v1.p1 (The database of Genotypes and Phenotypes, accession number: phs001918)<br> <br> <strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Chickpea flowering, carbon isotope, seed weight in a factorial of 20 genotypes and 8 environments
<p>Chickpea was phenotyped for time to flowering, carbon isotope composition at peak biomass, and seed weight at maturity in a factorial combining 20 genotypes, 2 sowing dates, 2 sowing regimes over two seasons. </p>
Nitrogen resorption dynamics and slow-fast strategies in 137 Arabidopsis thaliana genotypes
<p>Leaf nitrogen resorption efficiency (R_efficiency, %) and the relative maximum resorption rate of nitrogen (R_rate_max_perN, mg d<sup>-1</sup> mg<sup>-1</sup>) were estimated together with the flowering time (FT, days after germination) and specific leaf area (SLA, m<sup>2</sup> kg<sup>-1</sup>) in 137 Arabidopsis thaliana accessions selected from the 1001 genomes project accession list. The dataset contains genotype means for every measured accession.</p>
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data
<p>To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by (i) most published genomes being <1x coverage, (ii) ancient DNA fragments being typically <80 bps. These characteristics preclude state-of-the-art CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, an algorithm tailored for genotyping deletion and duplication events in genomes with low depths of coverage. Simulations and down-sampling experiments show that CONGA can genotype deletions >1 kbps with F-scores >0.75 at >=1x, and distinguish between heterozygous and homozygous states. Using CONGA, we analyse deletion events at 10,018 loci in 56 ancient human genomes spanning the last 50,000 years, with coverages 0.4x-26x. We show that inter-individual genetic diversity measured using deletions and SNPs are highly correlated, as in modern-day genomes, confirming that deletion frequencies broadly reflect demographic history. We also identify signatures of strong purifying selection on deletions in ancient-genomes, such as an excess of singletons compared to those in SNPs. CONGA paves the way for systematic studies of drift, mutation load, and adaptation in ancient and modern-day gene pools through the lens of CNVs.</p>
Development of a machine learning model to predict non- durable response to anti-TNF therapy in Crohn's disease using transcriptome imputed from genotypes
<p>This is the expression value predicted using PrediXcan version 7 to find a gene feature that can distinguish between patients with and without effect on infliximab.</p> <p>Among the various tissue models provided by PrediXcan v7, three models were selected and used: whole blood, Colon transverse, and terminal ileum of small intestine, and the predicted gene counts of each model were 6,294, 5,612 and 3,107.</p> <p>For each of the three models, predicted gene expression values and phenotype information per sample were submitted.</p>
Phenotypes and genotypes of brown trout used for breeding experiments in 2014
<p><span>Adult brown trout were caught via electrofishing around the beginning of the spawning season from the River Aare and its tributaries Gürbe, Worble, Giesse, Kiese, and Rotache (Bern canton, Switzerland). They were kept in the <em>Fischereistützpunkt Reutigen</em> until </span><span>eggs could be stripped from females</span><span>. Adults were </span><span>narcoticised when ready to spawn and gametes were stripped for block-wise full-factorial in vitro fertilisations (e.g. Marques da Cunha et al. 2019). Photographs were taken from all fish, standard length and wet weight were determined, and fin clips were taken for molecular analyses. All fish were then released back into the streams of origin. Samples of 24 freshly fertilized eggs per experimentally produced full-sib family were used for various laboratory experiments (e.g. Marques da Cunha et al. 2019). The remaining embryos were raised </span><span>in the <em>Fischereistützpunkt Reutigen</em> and used for stocking the streams of parental origin and various nursery streamlets, following the routine of the stocking program of the Bern canton. These stocked fish were later sampled at various stages of their life cycle, and 13 microsatellite markers could be used to assign these fish to their parents.</span></p> <p><span>Marques da Cunha L., Uppal A., Seddon E., Nusbaumer D., Vermeirssen E.L.M., Wedekind C. 2019. </span>No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout (<em>Salmo trutta</em>). Evol. Appl. 12(5), 940-950. (doi:10.1111/eva.12767).</p>
Patch quality and genotype-by-environment interactions shape dispersal and post-settlement survival in a butterfly metapopulation
Active dispersal is driven by extrinsic and intrinsic factors at the three stages of departure, transfer, and settlement. Most empirical studies capture only one stage of this complex process, and knowledge of how much can be generalized from one stage to another remains unknown. Here we use genetic assignment tests to reconstruct dispersal across five years and 232 patches of a butterfly metapopulation. We link individual dispersal events to weather, landscape structure, size and quality of patches, and individual genotype to identify the factors that influence the three stages of dispersal and post-settlement survival. We found that nearly all tested factors strongly affected departure probabilities, but that the same factors explained very little variation in realized dispersal distances. Surprisingly, we found no effect of dispersal distance on post-settlement survival. Rather, survival was influenced by weather conditions, carry-over effects of natal patch quality, and a strong interaction between genotype and occupancy status of the settled patch, with more mobile genotypes having higher survival as colonists rather than as immigrants. Our work highlights the multicausality of dispersal and that some dispersal costs can only be understood by considering extrinsic and intrinsic factors and their interaction across the entire dispersal process.
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file
<p>Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.</p> <p> </p> <p>File submitted correspond to the supplementary data 1 of the publication (under submission) : INRAE_USDA_MAF1.vcf.gz</p>
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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.
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DANDI Archive for NWB datasets
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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.