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”
The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns
Open the record for dataset details and reuse information.
Data from: A phased chromosome-level genome of the annelid tubeworm <em>Galeolaria caespitosa</em>
Open the record for dataset details and reuse information.
Data from: A de novo chromosome-level genome assembly of Coregonus sp. “Balchen”: one representative of the Swiss Alpine whitefish radiation
Open the record for dataset details and reuse information.
Range-wide study in a sexually polymorphic wild strawberry reveals climatic and soil associations of sex ratio, sexual dimorphism, and sex chromosomes
Open the record for dataset details and reuse information.
Topoisomerase IIA is essential for maintenance of mitotic chromosome structure
<p>Data files for the manuscript #2020-01760 "Topoisomerase IIA is essential for maintenance of mitotic chromosome structure" in press in the journal "Preceedings of the National Academy of Sciences" (PNAS).</p> <p> </p> <p>Abstract</p> <p>Topoisomerase IIa (TOP2A) is a core component of mitotic chromosomes and important for establishing mitotic chromosome condensation. The primary roles of TOP2A in mitosis have been difficult to decipher due to its multiple functions across the cell cycle. To more precisely understand the role of TOP2A in mitosis, we used the auxin inducible degron (AID) system to rapidly degrade the protein at different stages of the human cell cycle. Removal of TOP2A prior to mitosis does not affect prophase timing or the initiation of chromosome condensation. Instead, it prevents chromatin condensation in prometaphase, extends the length of prometaphase and ultimately causes cells to exit mitosis without chromosome segregation occurring. Surprisingly, we find that removal of TOP2A from cells arrested in prometaphase or metaphase cause dramatic loss of compacted mitotic chromosome structure and conclude that TOP2A is crucial for maintenance of mitotic chromosomes. Treatments with drugs used to poison/inhibit TOP2A function, such as etoposide and ICRF-193, does not phenocopy the effects on chromosome structure of TOP2A degradation by AID. Our data, points to a role for TOP2A as a structural chromosome maintenance enzyme component locking in condensation states once sufficient compaction is achieved.</p>
Data from: Chromosome-level genome of the melon thrips yields insights into evolution of a sap-sucking lifestyle and pesticide resistance
<p>Thrips are tiny insects from the order Thysanoptera (Hexapoda: Condylognatha), including many sap-sucking pests that are causing increasing damage to crops worldwide. In contrast to their closest relatives of Hemiptera (Hexapoda: Condylognatha) including numerous sap-sucking species, there are few genomic resources available for thrips. In this study, we assembled the first thrips genome at the chromosome level from the melon thrips, <i>Thrips palmi</i>, a notorious pest in agriculture, using PacBio long-read and Illumina short-read sequences. The assembled genome was 270.43 Mb in size with 4,120 contigs and a contig N50 of 426 kb. All contigs were assembled into 16 linkage groups assisted by the Hi-C technique. In total, 16,333 protein-coding genes were predicted, of which 88.13% were functionally annotated. Among sap-sucking insects, polyphagous species usually possess more detoxification genes than oligophagous species. The polyphagous thrips genomes characterized so far have relatively more detoxification genes in the GST and CCE families than polyphagous aphids, but they have fewer UGTs. HSP genes, especially from the Hsp70s group, have expanded in thrips compared to other hemipteran insects. These differences point to different genetic mechanisms associated with detoxification and stress responses in these two groups of sap-sucking insects. The expansion of these gene families may contribute to the rapid development of pesticide resistance in thrips, as supported by a transcriptome comparison of resistant and sensitive populations of <i>T. palmi</i>. The high-quality genome developed here provides an invaluable resource for understanding the ecology, genetics and evolution of thrips as well as their relatives more generally.</p>
Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings: To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage PacBio long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions: In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
Data from: Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (Aristelliger : Sphaerodactylidae)
<p>Current understanding of sex chromosome evolution is largely dependent on species with highly degenerated, heteromorphic sex chromosomes, but by studying species with recently evolved or morphologically indistinct sex chromosomes we can greatly increase our understanding of sex chromosome origins, degeneration, and turnover. Here, we examine sex chromosome evolution and stability in the gecko genus Aristelliger. We used RADseq to identify sex-specific markers and show that four Aristelliger species, spanning the phylogenetic breadth of the genus, share a conserved ZZ/ZW system syntenic with avian chromosome two. These conserved sex chromosomes contrast with many other gecko sex chromosome systems by showing a degree of stability among a group known for its dynamic sex determining mechanisms. Cytogenetic data from A. expectatus revealed homomorphic sex chromosomes with an accumulation of repetitive elements on the W chromosome. Taken together, the large number of female-specific A. praesignis RAD markers and the accumulation of repetitive DNA on the A. expectatus W karyotype suggests that the Z and W chromosomes are highly differentiated despite their overall morphological similarity. We discuss this paradoxical situation and suggest that it may, in fact, be common in many animal species.</p>
Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)
<p><span>We use genotyping by sequencing as an approach to identify sex-linked markers in the spiny frog <i>Quasipaa boulengeri</i> with 43 wild-collected adults from a single site. The GBS methodology identified 2 loci on sex differences in allele frequencies, 50 loci on sex differences in heterozygosity, and 523 loci on male-limited occurrence, altogether associated with males heterogamety, indicating an XX-XY system. The sex specificity of five markers was further validated by PCR amplification with a large number of additional individuals from 26 various populations in this species. A total of 27 sex linkage markers were matched to Dmrt1 gene, a ubiquitous role in sex determination and differentiation from flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has further been assigned to a highly potential candidate sex chromosome in anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133 individuals here, sparsely showing sex reversal detected in wild amphibian populations. </span></p>
Chromosome-level genome assembly of Poropuntius huangchuchieni
<p><i>Poropuntius huangchuchieni</i> is a diploid species in the family cyprinid, widely distributed in Mekong and Red River basins. Previous study suggested that it is one of the most closely related diploid ancestral species to common carp, which has allotetraploidized genome generated by merging two diploid genomes during evolution. Therefore, <i>P. huangchuchieni</i> is an ideal diploid model for polyploid evolution study in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of <i>P. huangchuchieni</i> by the integrating of the Oxford Nanopore Technology and Hi-C technology. The assembled genome size was 1021.38 Mb with a scaffold N50 of 32.93 Mb. More than 47.61% of the genome was identified as repetitive elements, and 895.66 Mb sequences were anchored onto 25 chromosomes. Of the 24,099 predicted protein-coding genes, 97.57% were functional annotated. Approximately 95.9% of complete BUSCOs were detected in the genome.The high-quality genomic data of <i>P. huangchuchieni</i> provides an ancestral diploid reference for the evolution and adaptation of allotetraploid carps.</p>
High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal
<p>The view genotypic sex determination (GSD) and environmental sex determination (ESD) are mutually exclusive states has been contradicted by the discovery that chromosomal sex and environmental influences can co-exist within the same species, hinting at a continuum of intermediate states. Systems where genes and the environment interact to determine sex present the opportunity for sex reversal to occur, where the phenotypic sex is the opposite of that predicted by their sex chromosome complement. The skink Bassiana duperreyi has XX:XY sex chromosomes with sex reversal of the XX genotype to a male phenotype in response to exposure to cold incubation temperatures. Here we studied the frequency of sex reversal in B. duperreyi in response to climatic variation, using elevation as a surrogate for environmental temperatures. We demonstrate sex reversal for the first time in free-ranging adults of a reptile species with XX/XY sex determination. The highest frequency of sex reversal occurred at the highest elevation location, Mount Ginini (18.64%) and decreases in frequency with elevation. We model the impact of this under Fisher's frequency dependent selection to show that, only at the highest elevations, populations risk the loss of the Y chromosome and a transition to TSD. This study contributes to our understanding of the risks of extinction from climate change in species subject to sex reversal by temperature, and will provide focus for future research to test on-the-ground management strategies to mitigate the effects of climate in local populations.</p> <div> <div> <div class="msocomtxt"> <p class="MsoCommentText"> </p> </div> </div> </div>
The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae)
<p>The genus <em>Rhododendron</em> (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of <em>Rhododendron williamsianum</em> as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the <em>R. williamsianum</em> genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in <em>R. williamsianum</em>. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in <em>Rhododendron</em> and <em>Vaccinium</em> (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.</p>
Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects
The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalisations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed this data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis, and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes and that orders exhibit striking differences in rates of fusions, fissions, and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.
Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths
<p>Here we provide scripts and parameters for genome assembly and annotation, as well as the manually annotated circadian genes of <i>period</i> (PER), <i>timeless</i> (TIM), <i>Clock</i> (CLK), <i>cycle</i> (CYC) and cryptochrome (CRY), five detoxification gene families of cytochrome P450 monooxygenase (P450s), glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs), UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC) transporters, IR, OR, OBP, GR genes from the genome of <span class="fontstyle01"><span>the peach fruit moth (PFM), </span></span><span class="fontstyle01"><span><i>Carposina sasakii</i></span></span><span class="fontstyle01"><span> Matsumura (Lepidoptera: Carposinidae, superfamily Copromorphoidea) and genomes of its related species.</span></span></p>
A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak
<p>Yak is an important livestock for the people who lived in harsh and oxygen-deprived Qinghai-Tibetan Plateau and Hindu-Kush Himalayan Mountains. Although there is a yak genome be sequenced in 2012, the assembly is quite fragmented due to the limitation of Illumina sequencing technology. An accurate and complete reference genome is critical for studying genetic variation of a specie. Long-read sequences are more complete than short-read ones, and they have been successfully used for high-quality genome assembly in several species. Here, we present a high-quality assembly of the yak genome (PB_v1.0) at chromosome scale, which was constructed using long-read sequencing technology assisted by chromatin interaction technology. Compared to the previous yak genome assembly (BosGru_v2.0), the PB_v1.0 assembly has substantially improved chromosome sequence continuity, minimized repetitive structure ambiguity, and achieved gene model completeness. To intensively characterize genetic variation of yak, we generated de novo genome assemblies based on Illumina short reads of seven recognized domestic yak breeds from Tibet and Sichuan as well as one wild yak from Hoh Xil. By comparing these eight assemblies to the PB_v1.0 genome, we obtained a comprehensive map of yak genetic diversity at whole genome level and identified a few protein-coding genes that were absent from the PB_v1.0 assembly. Although wild yak suffered bottleneck effect, the genetic diversity of wild yak is still higher than that of domestic yak. By whole genome alignment, we identified breed-specific sequences and genes, this will help the breeds identification of yak.</p>
Widespread recombination suppression facilitates plant sex chromosome evolution
<p>Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant <i>Rumex hastatulus</i>. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographical range. We identified the shared and neo-sex chromosome using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosome are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homologue indicates that low recombination rates preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing between repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.</p>
Supplementary Materials for "The Effects of Chromosome Doubling on Morphology, Salinity Tolerance, Essential Oil Composition, and Gene Expression of Biosynthesis Pathway in Peppermint (Mentha piperita L.)"
<p>Shandong Province Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; zhaozjfrances@163.com (Z.Z.); yanli_wei@163.com (Y.W.); menshenlai@163.com (K.Y.); sdkinghills@sina.com (B.L.); liling33802400@163.com (L.L.); yanght@sdas.org (H.Y)</p>
Data from: Chromosome inversions and ecological plasticity in the main African malaria mosquitoes
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.
Data from: Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants
Species with separate sexes (dioecy) are a minority among flowering plants, but dioecy has evolved multiple times independently in their history. The sex determination system and sex-linked genomic regions are currently identified in a limited number of dioecious plants only. Here, we study the sex-determination system in a genus of dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: <i>Nepenthes</i> pitcher plants. We genotyped wild populations of flowering males and females of three <i>Nepenthes</i> taxa using ddRAD-seq, and sequenced a male inflorescence transcriptome. We developed a statistical tool (privacy rarefaction) to distinguish true sex-specificity from stochastic noise in read coverage of sequencing data from wild populations and identified male-specific loci and XY-patterned SNPs in all three <i>Nepenthes</i> taxa, suggesting the presence of homomorphic XY sex chromosomes. The male-specific region of the Y chromosome showed little conservation among the three taxa, except for the essential pollen development gene DYT1 which was confirmed as male-specific by PCR in additional <i>Nepenthes</i> taxa. Hence, dioecy and part of the male-specific region of the <i>Nepenthes</i> Y-chromosomes likely have a single evolutionary origin.
Data from: Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.
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.