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3,457 results for “chromosomes”
Data for: "Chromosome One QTLs Associated with Beta Vulgaris Response to Bacterial Leaf Spot"
<p>Listed here are data used in analysis for publication "Chromosome One QTLs Associated with Beta Vulgaris Response to Bacterial Leaf Spot".</p> <p>Data included: filtered VCF files of SNP marker data for full Wisconsin Beta Diversity Panel (WBDP, n=219) and table beet subset (n=152). Deposited also are the raw phenotypic values, the final weighted BLS score per pot, the BLUE value for each accession, and the leaf color covariate data.</p>
Fig. 2 in Allopatric chromosomal variation in Nematocharax venustus Weitzman, Menezes & Britski, 1986 (Actinopterygii: Characiformes) based on mapping of repetitive sequences
Fig. 2. Representative karyotype of Nematocharax venustus. Bar = 5 µm.
Fig. 2. Karyotypes showing C in Microstructural chromosome reorganization in the genus Trichomycterus (Siluriformes: Trichomycteridae)
Fig. 2. Karyotypes showing C Band of the species of Trichomycterus analyzed.
Fig. 1 in Microstructural chromosome reorganization in the genus Trichomycterus (Siluriformes: Trichomycteridae)
Fig. 1. Karyotypes of Trichomycterus species analyzed showing chromosomes after Giemsa.
Additional files for Hegyi and Lexa, 2024. Y chromosome-coded HSATII repeats may contribute to higher incidence of cancer in men.
<p>Additional data for Hegyi and Lexa, 2024 (scripts, data, supplementary figures, tables and files).</p>
R codes prepared for the manuscript, entitled "The roles of Y chromosomal genes in mouse sex spectrum phenotypes"
<p>R codes for the manuscript, entitled "The roles of Y chromosomal genes in mouse sex spectrum phenotypes" </p>
FIGURE 1 in Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae
FIGURE 1 | Map of Ecuador, highlighting the sampling site of Saccodon wagneri.
Similarity of CRISPR genes grouped by chromosome location with chromosome arm correction
Open the record for dataset details and reuse information.
Similarity of CRISPR genes grouped by chromosome location without chromosome arm correction
Open the record for dataset details and reuse information.
Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)
<p>Genomic datasets generated from three species of psyllid insect (Hemiptera: Psylloidea). This repository includes chromosome-scale genomic assemblies, mitochondrial genomes, co-assembled bacterial genomes, coding sequence annotations, transposable element annotations, and called SNPs, as well as files related to comparative genomics analyses. </p> <p><strong>Dataset contains:</strong><br><strong>From Trioza urticae genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - T. urticae derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From Dyspersa pallida (Trioza anthrisci) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. pallida mitochondrial genome assembly (fasta)<br> - D. pallida derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From Dyspersa apicalis (Trioza apicalis) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. apicalis mitochondrial genome assembly (fasta)<br> - D. apicalis derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From comparative genomics analysis:</strong><br> - Orthofinder analysis<br> - - Output of orthofinder analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (tsv and fasta)<br> - Cafe5 analysis<br> - - Output of cafe analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (excel, png, tab)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the Dyspersa taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. pallida taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. apicalis taxonomic node (excel and tiff)<br> - - - Plots showing expansion/contraction of different orthogroups across the hemiptera phylogeny (png)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by iqtree2 (txt)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by astral (txt)<br> - C. Ca ruddii primary endosymbiont phylogenetic tree (txt)</p> <p><strong>From psyllid population resequencing:</strong><br> - Resequencing data<br> - - High confidence biallelic SNPs from D. pallida resequenced samples called against the de novo D. pallida genome assembly (vcf)<br> - - High confidence biallelic SNPs from D. apicalis resequenced samples called against the de novo D. apicalis genome assembly (vcf)<br> - - High confidence biallelic SNPs from resequenced samples called against the reference C. Ca ruddi endosymbiont genome assembly (vcf)<br> - - For suspected contanimant contigs removed from the D. pallida genome assembly; predicted identity, and coverage in each resequenced D. pallida sample (txt)<br> - - For suspected contanimant contigs removed from the D. apicalis genome assembly; predicted identity, and coverage in each resequenced D. apicalis sample (txt)<br> - - - Qualimap evaluation of resequencing data aligned to de novo psyllid genome for each resequenced sample (pdf)<br><br><br></p>
Assemblies and annotations from the paper "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses"
<div> <p>This repository contains the whole genome assemblies, gene and TE annotations generated and analyzed in the manuscript entitled "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses". </p> <p>Preprint available on BioRxiv:</p> <p>https://www.biorxiv.org/content/10.1101/2024.10.03.616481v1</p> <p> </p> </div>
Frequency maps of Y-chromosomal haplogroups in Finland - out of major haplogroup
<p>Y-chromosomal regional enrichment maps for all haplogroups with at least 1% frequency in Finland out of major haplogroup carriers (N1a1, I1a, R1a and R1b). A star (*) within the map and gray color in the forest plot indicates the frequency is inferred by combining samples from geographically closest regions due to low coverage of samples in the region.</p>
Metadata of Y chromosome samples from Karmin et al. plus the Tyrolean Iceman
<p>The ID, country, and mutation count for 130 Y chromosome samples. Iceman's added to 129 samples from Karmin et al. 2015 Y chromosome dataset:</p> <p>Karmin, M., L. Saag, M. Vicente, M. A. W. Sayres, M. Järve, U. G. Talas, S. Rootsi, A. M. llumäe, R. Mägi, M. Mitt, L. Pagani, et al. 2015. “A Recent Bottleneck of Y Chromosome Diversity Coincides with a Global Change in Culture.”<span> </span><em>Genome Research</em><span> </span><em>25, no. 4 (April): 459–466</em>.</p> <p>The mutation counts are relative to Noah's assumed sequence, based on the major allele at each position in the VCF file, also available in this repository.</p>
Three-point contact data for "Multi-contact statistics distinguish models of chromosome organization"
<p>Three-point contact data for the publication "Multi-contact statistics distinguish models of chromosome organization".</p>
Data from: Simulating effects of fitness and dispersal on the use of Trojan sex chromosomes for invasive species management
<ol> <li>The use of Trojan Y Chromosomes (TYC) for controlling invasive species involves manipulating the sex chromosomes of captive-raised individuals. Once released, the offspring of these individuals consist of only one sex, thereby skewing the sex-ratio of the invasive population and potentially leading to eradication. Simulation models are needed that can inform managers on how to maximize the likelihood of species eradication, since implementation of this novel management approach in the field is still rare.</li> <li>Here, we present the first spatially explicit, mechanistic simulation model of a real-world TYC program for invasive species eradication. Using a brook trout (Salvelinus fontinalis) system model, we investigated the effects of competitive and reproductive fitness of the captive-raised YY males, dispersal behavior upon their release, and landscape heterogeneity on eradication success.</li> <li>Likelihood of eradication was dependent on both the competitive and reproductive fitness of the Trojan individuals. Competitive fitness (i.e., survival) had a higher threshold for eradication, below which populations failed to be eradicated.</li> <li>Movement ecology of both the wild and YY male populations was important for eradication. Under a restricted dispersal scenario for YY males following their release, the wild population was not extirpated but maintained a stable, yet reduced, population size. In terms of landscape configuration, time to eradication of local patches increased with greater connectivity within the stream network.</li> <li>In addition to sex ratio distortion, density-dependent mortality resulting from outplantings made an important contribution to eradication and therefore may also affect native competitors.</li> <li>While our results indicate that eradication is possible, maximizing its likelihood requires an understanding of the fitness and movement ecology of both the wild and YY male populations of the invasive species. Both our model and the principles derived from this study related to fitness and behavioral landscape ecology can be broadly applied to other invaded species and systems.</li> </ol>
Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals
<p><span>Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera <i>Microcebus</i> and <i>Cheirogaleus</i>, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, </span>as might be expected if they have each evolved to respond to specific stimuli<span>. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus <i>Mus</i>) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."</span></p>
Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)
<p>The study used genetic mapping and coverage data in genome sequences of multiple male and female individuals of <i>M. picta</i> from multiple natural populations to investigate genetic degeneration of the Y chromosome, and quantify gene loss from the Y. The files include coverage results from the sex chromosome that were (i) used for sexing the sequenced individuals, and (ii) combined with autosomal results to analyze M/F, M/A and F/A depth of coverage ratios. Genetic mapping was also used to validate sex linkage, and the data set includes files with genotypes of genetic markers.</p>
Fig. 35 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 35. Closeup dorsal views of a medial circumvallate papilla in A. Noctilio leporinus (AMNH
Fig. 3 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 3. Tree from Wenzel et al. (1966; redrawn from fig. 144) by de la Torre.
Fig. 1 in Chromosomal characterization of the bonytongue Arapaima gigas (Osteoglossiformes: Arapaimidae)
Fig. 1. Karyotype of Arapaima gigas showing chromosome constrictions in pair 3. Bar = 5 µm.
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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.