Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,457
datasets available to search
ShareScore release 0.7.1
Dataset results
3,457 results for “chromosomes”
Figure 1 in Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap?
Figure 1. Parsimony analysis of sex-determining mechanisms in squamate reptiles based on the 'morphological' tree. Circles indicate maximum-likelihood reconstructions of ancestral states, only nodes with significant reconstruction are shown (tested by likelihood-ratio test). Numbers in parentheses indicate the counts of species within a genus that share
Example variant files and corresponding annotations for GnomAD v3.1.1 on a subset of chromosome 22
<p>Example variant files and corresponding hg38 annotations for `chr22:15518158-20127355`.</p> <p>Sources:</p> <ul> <li><a href="http://dx.doi.org/10.1093/nar/gky955">Gencode v34 (hg38)</a></li> <li><a href="https://doi.org/10.1038/s41586-020-2308-7">GnomAD v3.1.1</a></li> </ul>
Data from: Female-limited X-chromosome evolution effects on male pre- and post-copulatory success
<p>In our article, entitled "Female-limited X-chromosome evolution effects on male pre- and post-copulatory success", we carried out a female-limited X chromosome evolution experiment to study the effect of X-linked sexually antagonistic genetic variance on male reproductive traits.</p> <p>By limiting expression of the X chromosome to females for multiple generations, we removed male selective constraints, which should allow X-linked female-beneficial alleles to increase in frequency. </p> <p>As a result, expressing the experimentally evolved X chromosome in males, we found a small reduction in male fitness caused by the trade-off between male attractiveness and sperm competitiveness. These results indicate that the X chromosome in <i>D. melanogaster</i> harbors sexually antagonistic genetic variance for pre- and post- copulatory success in males.</p>
Epistatic interactions between sex chromosomes and autosomes can affect the stability of sex determination systems
<p>Sex determination (SD) is an essential and ancient developmental process, but the genetic systems that regulate this process are surprisingly variable. Why SD mechanisms vary so much is a longstanding question in evolutionary biology. SD genes are generally located on sex chromosomes which also carry genes that interact epistatically with autosomes to affect fitness. How this affects the evolutionary stability of SD mechanisms is still unknown. Here, we explore how epistatic interactions between a sexually antagonistic (SA) non-SD gene, located on either an ancestral or novel sex chromosome, and an autosomal gene affect the conditions under which an evolutionary transition to a new SD system occurs. We find that when the SD gene is linked to an ancestral sex chromosomal gene which engages in epistatic interactions, epistasis enhances the stability of the sex chromosomes so that they are retained under conditions where transitions would otherwise occur. This occurs both when weaker fitness effects are associated with the ancestral sex chromosome pair or stronger fitness effects associated with a newly-evolved SD gene. However, the probability that novel SD genes spread is unaffected if they arise near genes involved in epistasis. This discrepancy occurs because on autosomes, SA allele frequencies are typically lower than on sex chromosomes. In our model, increased frequencies of these alleles contribute to a higher frequency of epistasis which may therefore more readily occur on sex chromosomes. Because sex chromosome-autosome interactions are abundant and can take several forms, they may play a large role in maintaining sex chromosomes.</p>
Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata
<p><em>Quercus dentata</em> Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for <em>Q. dentata</em>. This 893.54 Mb sized genome (contig N50=4.21 Mb, scaffold N50=75.55 Mb; 2n=24) harbors 31,584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) <em>QdNAC </em>(<em>QD08G038820</em>) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, <em>QdMYB </em>(<em>QD01G020890</em>), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome and transcriptome resources further enrich <em>Quercus </em>genomics, and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.</p>
Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome
<p>Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatric <em>Drosophila virilis</em> group species, <em>D. flavomontana </em>and<em> D. montana</em>. We backcrossed F<sub>1</sub> hybrid females from a cross between <em>D. flavomontana female </em>and<em> D. montana </em>male with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal 2<sup>nd</sup> generation backcross (BC<sub>2</sub>mon and BC<sub>2</sub>fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC<sub>2</sub> female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC<sub>2</sub>mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towards <em>D. montana</em>. In contrast, the BC<sub>2</sub>fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). We find that this observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.</p>
Additional annotation, alignment, and results from Ka/Ks analysis for Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus)
<p><strong>Annotation files, alignments, and results summaries from Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus).</strong></p> <p>Pairwise genome alignments contain the .maf suffix</p> <p>FASTA alignments from stitched gene blocks contain the .fasta suffix</p> <p>CSV file containing the Ka/Ks results</p> <p>RepeatMasker .out file</p>
Data from: The origin of a new chromosome in gerbils
<p><span>Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil (<em>Meriones unguiculatus</em>) have distinct underpinnings: chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats (probably due to centromeric drive); while chromosome 13 is comprised of extremely large (>150kb) repeated sequences. We suggest that chromosome 13 originated when a functionally important 'seed' broke off from another chromosome and underwent multiple breakage-fusion-bridge cycles. Genes with the most extreme GC skew are encoded on this chromosome, most likely due to the restriction of recombination to a narrow permissive region (since GC bias is linked with recombination-associated processes). Our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data, and highlight novel patterns involved in the evolution of chromosomes.</span></p>
Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.
<p>We assembled and annotated a new, long-read genome assembly for ‘Carlos’, a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We are awaiting release of the genome through NCBI, so we have made the assembly and annotations available here.</p>
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
<p>This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (<em>Eleginops maclovinus</em>), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the <em>E. maclovinus </em>genome, the dataset includes a description of circadian rhythm orthologs for <em>E. maclovinus</em>, other notothenenioid taxa, and teleost outgroups, as well as a copy of the bioinformatic scripts used for the assembly, annotation, and other downstream analysis.</p>
Figs 7–8. Silver nitrate-stained Turkonalassus quercanus meiotic chromosomes. 7 in Cytogenetic analysis on Turkonalassus quercanus Keskin, Nabozhenko et Alpagut-Keskin, 2017 (Coleoptera: Tenebrionidae: Helopini)
Figs 7–8. Silver nitrate-stained Turkonalassus quercanus meiotic chromosomes. 7 – Xyp sex bivalent in male MI plate (arrow indicates argyrophilic sex bivalent); 8 – a prominent nucleolus associated with one of the medium sized chromosomes, and pericentromeric heterochromatin regions seen as smaller dots in prophase I chromosomes. Scale bars 5 µm. Рис. 7–8. Мейотические хромосомы Turkonalassus quercanus, окашенные нитратом серебра. 7 – поΛовой биваΛент Xyp на пΛастинке MI самца (стреΛка указывает на аргирофиΛьный поΛовой биваΛент); 8 – заметное яΑрышко, связанное с оΑной из хромосом среΑнего размера, и перицентромерные обΛасти гетерохроматина в виΑе боΛее меΛких точек в хромосомах профазы I. Масштабные Λинейки 5 µm.
Genomic insights into the chromosomal elongation in a family of Collembola
<p>Collembola is a highly diverse and abundant group of soil arthropods with chromosome numbers ranging from 3 to 11. Tomoceridae is one of the oldest collembolan families, and previous karyotype studies indicated that this family possesses an exceptionally long chromosome. To better understand chromosome size evolution in Collembola, we obtained a chromosome-level genome of <em>Yoshiicerus persimilis</em> with a size of 334.44 Mb and BUSCO completeness of 97.0%. Both genomes of <em>Y. persimilis </em>and <em>Tomocerus qinae</em> (recently published) have an exceptionally large chromosome (ElChr>100 Mb), accounting for nearly one-third of the genome. Comparative genomic analyses revealed a high degree of homology between the two ElChr, with 95.08% (2,224) of 1:1:1 orthologous genes shared between them. The ElChr elongation was caused by segmental duplication and transposon proliferation, with genes in these regions experiencing stronger selection pressure (higher dN/dS) than conserved regions. Enrichment analysis revealed that duplicated genes of ElChr were primarily associated with proliferation and growth, which explains their larger body size. Moreover, inter-genomic synteny analyses indicated that chromosomal fission/fusion events played a crucial role in the evolution of chromosome numbers within Entomobryomorpha. This study provides important insights into the mechanisms of chromosome evolution and offers a valuable omics resource for Collembola.</p>
Annotation Data: Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: A Resource for fungal biology and biotechnology
<p><strong>Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: A Resource for fungal biology and biotechnology</strong></p> <p>Genome annotation data</p> <p><strong>Genome Browser:</strong> <a href="https://plantgenomics.ncc.unesp.br/gen.php?id=Asub">https://plantgenomics.ncc.unesp.br/gen.php?id=Asub</a></p>
Near-Chromosomal-Level Genome of the Red Palm Weevil (Rhynchophorus ferrugineus), a Potential Resource for Genome-Based Pest Control.
<p>Red palm weevil genome annotation data set</p>
Figure 2 in New insights into the chromosomal differentiation patterns among cichlids from Africa and Madagascar
Figure 2. – Karyotypes of Malagasy and African cichlids after conventional fluorescence in situ hybridization counterstained with DAPI (blue). m/sm pairs are separated on the first line of each karyotype. The 18S rRNA probed chromosomes are shown (red). Scale bar = 5 µm.
Study of Nilotinib as First Line Treatment in Philadelphia Chromosome Positive(Ph+) Chronic Myelogenous Leukemia in Chronic Phase (CML-CP)
ClinicalTrials.gov study NCT01274351. IPD Sharing: YES. Countries: 1. Publications: 2.
A Study of Imatinib Versus Nilotinib in Adult Patients With Newly Diagnosed Philadelphia Chromosome Positive (Ph+) Chronic Myelogenous Leukemia in Chronic Phase (CML-CP)
ClinicalTrials.gov study NCT00471497. IPD Sharing: YES. Countries: 35. Publications: 8.
Novel fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes
Open the record for dataset details and reuse information.
High quality, chromosome-scale genome assemblies: Comparisons of three Diaphorina citri (Asian Citrus Psyllid) geographic populations
Open the record for dataset details and reuse information.
Data from: The origin of a new chromosome in gerbils
Open the record for dataset details and reuse information.
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.