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3,457 results for “chromosomes”
Figure 3 in Chromosomal separation of difficult species of Copris Geoffroy, 1762 and Onthophagus Latreille, 1802 (Coleoptera, Scarabaeidae), with discussion of O. massai Baraud as a British Pleistocene fossil
Figure 3. Mitotic chromosomes of Onthophagus fracticornis (a – l) and O. massai (m, n), arranged as karyotypes. a, c, e, g, i, k, m, plain, b, d, f, h, j, l, n, the same nuclei C-banded. a, b, Spain; c, d, England; e, f, Macedonia, Šar Planina; g, h, Macedonia, Mavrovo National Park, with one B-chromosome and autosome 5 heterozygous for a pericentric inversion; i, j, Czech Republic; k, l, Italy; m, n, Sicily, Piano Zucchi.
Figure 2 in Chromosomal separation of difficult species of Copris Geoffroy, 1762 and Onthophagus Latreille, 1802 (Coleoptera, Scarabaeidae), with discussion of O. massai Baraud as a British Pleistocene fossil
Figure 2. Mitotic chromosomes of Copris hispanus hispanus (a, b) and C. h. cavolinii (c, d) arranged as karyotypes. a, c, plain, b, d, the same nuclei C-banded.
A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum (Hausman) (Hemiptera: Aphididae)
<p><strong><em>Eriosoma lanigerum</em> v1.0 frozen release</strong></p> <p>Genome assembly: Eriosoma_lanigerum.v1.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Eriosoma_lanigerum.v1.0.scaffolds.gff</p> <p>BRAKER2 protein sequences: Eriosoma_lanigerum.v1.0.scaffolds.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Eriosoma_lanigerum.v1.0.scaffolds.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Eriosoma_lanigerum.v1.0.scaffolds.gff.cds.fa</p> <p><em>Buchnera aphidicola</em> scaffolds: Buchnera_aphidicola.scaffolds.fa</p> <p><strong>Aphid orthogroups</strong></p> <p>OrthoFinder run files (see for details <a href="https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf">https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf</a>): OrthoFinder_run.tar.gz</p>
Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild
<p>Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (<i>Oryx dammah)</i> is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large‐scale and long‐term reintroduction project. To enable the selection of suitable founder individuals, facilitate post‐release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi‐C contact mapping to develop a chromosomal‐level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar‐horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.</p>
Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark
Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species.
Chromosome-scale assembly of winter oilseed rape Brassica napus
<p>The files correspond to data and results referenced in research article titled "Chromosome-scale assembly of winter oilseed rape Brassica napus".</p> <p>Data files below were used in the scaffolding process of genome assembly:</p> <ol> <li>Genetic maps (csv) <ul> <li>ExR53-DH_60kSNPmap</li> <li>ExV8-DH_60kSNPmap</li> </ul> </li> </ol> <p>Result files below are assembled sequences of the genome and the predicted annotation:</p> <ol> <li>Genome assembly (Express617_v1.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_cds.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_gene.gff3.gz)</li> <li>Predicted protein sequences (Express617_v1_protein.fa.gz)</li> <li>Predicted repetitive elements (Express617_v1_repeats.gff.gz)</li> </ol>
Chromosome images used for "Centromere detection of human metaphase chromosome images using a candidate based method"
<p>Chromosome image data used in the paper "Centromere detection of human metaphase chromosome images using a candidate based method". Images are in tiff format</p>
Chromosome images used for "Centromere detection of human metaphase chromosome images using a candidate based method"
<p>Chromosome image data used in the paper "Centromere detection of human metaphase chromosome images using a candidate based method". Images are in tiff format.</p>
Drosophila simulans LD results from PLINK for Chromosome X
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and dataset</strong>s: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 3L, and 4.</p>
Drosophila simulans LD results from PLINK for Chromosome 3R
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3L, 4, and X.</p>
Drosophila simulans LD results from PLINK for Chromosome 4
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Wor</strong>k: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 3L, and X.</p>
Drosophila simulans LD results from PLINK for Chromosome 2R
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Wor</strong>k: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 3L, 3R, 4, and X.</p>
Drosophila simulans LD results from PLINK for Chromosome 3L
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R, 3R, 4, and X</p>
Drosophila simulans LD results from PLINK for Chromosome 2L
<p><strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p> <p><strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). </p> <p><strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.</p> <p><strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2R, 3L, 3R, 4, and X.</p>
Direct chromosome-length haplotyping by single-cell sequencing.
<p>Selected Strand-seq libraries from PMID:27646535 study. Data were originally shared on the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under the accession number: PRJEB14185</p>
Single-cell mouse and PC9 data for "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability"
<p>This repository includes the processed data (including copy number profiles and related analysis) for the E/EP mouse tumors and for the PC9 resistance cell lines for all the analyses of the manuscript "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability".</p><p>The code for the related analyses is available in GitHub at https://github.com/zaccaria-lab/TP53loss_WGD</p>
Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation
<p>When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (<em>Zonotrichia atricapilla</em>) and the white-crowned sparrow (<em>Zonotrichia leucophrys</em>) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of <em>Z. leucophrys</em>. The two <em>Z. leucophrys</em> subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species <em>Z. leucophrys</em> and <em>Z. atricapilla</em> show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between <em>Z. atricapilla</em> and <em>Z. leucophrys</em> appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.</p>
Sex chromosomes and hormones independently influence healthy brain development but act similarly after cranial radiation
<h2><strong>Description</strong></h2> <p>Biological sex influences prevalence of developmental disorders through sex hormones and sex chromosomes. However, our understanding of their impacts in neurodevelopment and response to injury remains limited. In this project, we use high resolution magnetic resonance imaging (MRI) to investigate the four core genotype mouse model (FCG) that separates the influences of sex hormones and sex chromosomes during normal brain development and after cranial radiation therapy. </p> <p>Sex differences are attributed to either sex hormones or sex chromosomes. This can be distinguished by the FCG model which decouples the sex determining region (SRY) from the Y chromosome by moving SRY onto an autosome. This gives us four core sex genotypes: XX NULL, XY NULL, XX SRY, and XY SRY.</p> <p>This dataset represents the <em>most comprehensive mouse brain imaging study</em> employing the FCG model to date with 5 timepoints (P14, P23, P42, P63, P98), Ccl2 wildtype (+/+) and knockouts (-/-), irradiation (7Gy) and sham (0Gy) mice. All in all, a total of <strong>1071 images</strong>! The results presented here is published in PNAS.</p> <p>In vivo MRI scans were obtained using a 7-T MRI scanner (Bruker BioSpin, Ettlingen, Germany) equipped with four cryocoils for simultaneous imaging of four mice. The scans were performed with the following settings: T1-weighted, 3D-gradient echo sequence, 75μm isotropic resolution, TR=26ms, TE=8.25ms, flip angle=26°, field of view=25×22×22mm, and matrix size=334×294×294.</p> <p>All structural MR images are stored in <strong>images.tar.gz</strong>. Images were segmented and registered using an automated pipeline which are stored in <strong>labels.tar.gz</strong>. The consensus average and labels are <strong>final_average.mnc </strong>and <strong>final_labels.mnc</strong>, respectively. Extracted structure volumes alongside the metadata are included in <strong>df_micevolumes.csv</strong>. Structural MRIs are in MINC format and the <strong>readme.txt</strong> provides further information on this dataset. </p> <p>The authors express their sincere gratitude for the research funding recieved from the Canadian Institutes of Health Research (158622, 168037) and the Ontario Institute for Cancer Research (IA-024) with funding from the Government of Ontario and Restracomp from the SIckKids Research Training Centre.</p> <p><strong>Publication</strong>: https://www.pnas.org/doi/10.1073/pnas.2404042121</p> <h2><strong>Code/Software </strong></h2> <p><strong>MINC</strong><br>https://www.bic.mni.mcgill.ca/ServicesSoftware/MINC</p> <p><strong>RMINC</strong><br>https://github.com/Mouse-Imaging-Centre/RMINC</p> <p><strong>PydPiper</strong><br>https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.19.1</p>
Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities
<h2>The Id locus, with a potential polygenic nature, is inverted alongside ZARU1 at the distal end of the q-arm of chromosome Z, indicating a shared ancestry among BBC breeds.</h2>
Sequencing a botanical monument: a chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.) at the Botanical Garden of the University of Padua (Italy)
<p>The enclosed data pertains to the genome assemblies of the mitochondrion (final_mitogenome.fasta) and the plastid (plastid_genome.fasta) of the dwarf palm <em>Chamaerops humilis</em> L.</p> <p><strong><em>Please refer to the published paper for further details.</em></strong></p>
ScienceDex guides
Understand access before you commit
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.