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3,457 results for “chromosomes”
A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)
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Phylogenetics, taxonomy, and chromosome number analysis of Sanvitalia (Asteraceae-Heliantheae-Zinniinae)
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Data from: The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals
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A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes
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Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila
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Chromosome walking
<p>The complete project folder that includes all datasets and code used to produce the results described in <a href="https://www.mdpi.com/2076-3417/11/8/3511">Vernone et al. 2020</a>, "<a href="https://www.mdpi.com/2076-3417/11/8/3511">Chromosome Walking: A Novel Approach to Analyse Amino Acid Content of Human Proteins Ordered by Gene Position</a>"</p>
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
FIG. 7 in Comparative chromosomal studies in Rhinolophus formosae and R. luctus from China and Vietnam: elevation of R. l. lanosus to species rank
FIG. 7. Metaphase spreads of R. formosae after CBG-banding (A, B) and silver-staining (C). A — Centromeric heterochromatin is clearly visible at acrocentric chromosomes but only faintly stained at the metacentric ones. The arrows point to the smallest autosomal pair no. 25 which is presumably bi-armed. B — The C-banded X chromosomes of the female R. formosae showed the usual appearance for the family without a large hetero-chromatic block. The arrows indicate pair 25. C — Silver-stained metaphase plate with arrows indicating the NORs
FIG. 3 in Comparative chromosomal studies in Rhinolophus formosae and R. luctus from China and Vietnam: elevation of R. l. lanosus to species rank
FIG. 3. FISH examples showing the hybridization patterns of A. stoliczkanus (AST) chromosome-specific painting probes onto metaphase spreads of R. cf. luctoides (A, D), R. lanosus (B, E) and R. formosae (C, F). A–C — hybridization signals of AST1 (red) and AST8 (green) meet in chromosome 5 in R. cf. luctoides (A) and R. lanosus (B) but not in R. formosae (C). In B and C AST X (yellow) was applied in addition. D, E — hybridization signals of AST2 (green) and AST5 (red) meet in chromosome 3 of R. cf. luctoides (D), but not in R. lanosus (E), where AST2 (green) is found in combination with AST1 (red) on chromosome 4 instead.
"The evolutionary history of Neandertal and Denisovan Y chromosomes" - hg20 mapping of the capture data
<p>This archive contains the alignments of all individuals captured with the 6.9 Mb array mapped to GRCh38/hg20. See the project's GitHub repository for more information: <a href="https://www.github.com/bodkan/archaic-ychr">https://www.github.com/bodkan/archaic-ychr</a>.</p>
Dataset for CHISEL complete demo on chromosome 6
<p>This dataset contains all the files required for the complete demo of CHISEL on chromosome 6. Specifically, the files included here are:</p> <ol> <li>`cells.bam` barcoded BAM file (using flag `CB:Z:[A,C,G,T]+`) for 100 tumor single cells;</li> <li>`cells.bam.bai` index of the barcoded BAM file;</li> <li>`normal.bam` matched-normal BAM file for the 100 tumor single cells;</li> <li>`normal.bam.bai` index of the matched-normal BAM file.</li> <li>'phases.tsv' tab-separated dataframe with phases of germline SNPs, with fields `CHROMOSOME POS PHASE`</li> </ol>
Dataset for CHISEL pseudonormal demo on chromosome 6
<p>This dataset contains all the files required for the pseudonormal demo of CHISEL on chromosome 6. Specifically, the files included here are:</p> <ol> <li>`cells.bam` barcoded BAM file (using flag `CB:Z:[A,C,G,T]+`) for 40 single cells, with 30 tumor cells and 10 normal cells;</li> <li>`cells.bam.bai` index of the barcoded BAM file;</li> </ol>
Data from: Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum
<p>Naturally occurring autopolyploid species such as the autotetraploid potato <i>Solanum tuberosum</i> face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid <i>S. tuberosum</i> using fluorescence <i>in situ</i> hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7-48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of <i>S. tuberosum</i> as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.</p>
Data from: Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies
<p>Sex chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inferences. Rapidly evolving complex sex chromosome systems represent a rare opportunity to study the mechanisms of sex chromosome evolution at unprecedented resolution. Three cryptic species of wood white butterflies – <i><span>Leptidea juvernica</span></i>, <i><span>L. sinapis</span></i>, and <i><span>L. reali</span></i> – have each a unique set of multiple sex chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray for comparative genomic hybridization (array-CGH) and a library of bacterial artificial chromosome (BAC) clones, both developed in <i><span>L. juvernica</span></i>, we identified Z-linked <i><span>Leptidea</span></i> orthologs of <i><span>Bombyx mori</span></i> genes and mapped them by fluorescence <i><span>in situ</span></i> hybridization (FISH) with BAC probes on multiple Z chromosomes. In all three species, we determined synteny blocks of autosomal origin and reconstructed the evolution of multiple sex chromosomes. In addition, we identified W-homologs of Z-linked orthologs and characterized their molecular differentiation. Our results suggest that the multiple sex chromosome system evolved in a common ancestor of these three <i><span>Leptidea</span></i> species as a result of dynamic genome reshuffling through repeated rearrangements between the sex chromosomes and autosomes, including translocations and fissions. Thus, the sex chromosome turnover could not play a role in reproductive isolation between the <i><span>Leptidea </span></i>species studied. However, we suggest that subsequent species-specific rearrangements of multiple sex chromosomes, along with different rates of neo-W chromosome degeneration and significantly increased number of Z-linked genes could accelerate the accumulation of genetic incompatibilities between populations and promote their divergence resulting in speciation.</p>
Data from: Sperm quality, aggressiveness and generation turnover can facilitate unidirectional Y chromosome introgression across the European house mouse hybrid zone
The widespread and locally massive introgression of Y chromosomes of the eastern house mouse (<i>Mus musculus musculus</i>) into the range of the western subspecies (<i>M. m. domesticus</i>) in Central Europe calls for an explanation of its underlying mechanisms. Given the paternal inheritance pattern, obvious candidates for traits mediating the introgression are characters associated with sperm quantity and quality. We can also expect traits such as size, aggression, or the length of generation cycles to facilitate the spread. We have created two consomic strains carrying the non-recombining region of the Y chromosome of the opposite subspecies, allowing us to study introgression in both directions, something impossible in nature due to the unidirectionality of introgression. We analysed several traits potentially related to male fitness. Transmission of the <i>domesticus</i> Y onto the <i>musculus</i> background had negative effects on all studied traits. Likewise , <i>domesticus</i> males possessing the <i>musculus</i> Y had, on average, smaller body and testes and lower sperm count than the parental strain. However, the same consomic males tended to produce less dissociated sperm heads, to win more dyadic encounters, and to have shorter generation cycles than pure <i>domesticus</i> males. These data suggest the <i>domesticus</i> Y is disadvantageous on the <i>musculus</i> background while introgression in the opposite direction can confer a recognizable, though not always significant, selective advantage. Our results are thus congruent with the unidirectional <i>musculus</i>→domesticus Y chromosome introgression in Central Europe. In addition to some previous studies, they show this to be a multifaceted phenomenon demanding a multidisciplinary approach.
Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species
<p><span><span><span><span><span><span><span><span><span><span><span>Genetic and physical mapping of the guppy (<i>P. reticulata</i>) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in of pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We here used the intronic GC content to indirectly infer the recombination patterns on guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3<sup>rd</sup> positions of codons, in order to make comparisons between sequences that are matched, as far as possible, with respect to selective constraints. Both these types of sites are likely to be under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), prove to have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (<i>Xiphophorus maculatus</i>). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of guppy chromosomes, which were not determined in the guppy genome assembly. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks
<p>Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their non-independence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P<sub>1</sub>,P<sub>2</sub>),P<sub>3</sub>),Out) and a matrix of pairwise nucleotide divergence (d<sub>XY</sub>) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide-breath of parameter space. We then used HyDe-CNN to test models of admixture in <em>Heliconius</em> butterflies, as well as comparing it to a random forest classifier trained on introgression-based statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing, and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.</p>
Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>Background: Plants exhibit wide chemical diversity due to production of specialized metabolites which function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs and as sources of insect repellents, health-promoting compounds, and fragrance. Findings: We report the chromosome-scale genome assembly of <em>Callicarpa americana</em> L. (American beautyberry), a species within the early diverging Callicarpoideae clade of the Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long reads and Hi-C scaffolding, we generated a 506.1 Mb assembly spanning 17 pseudomolecules with an N50 contig and N50 scaffold size of 7.5 Mb and 29.0 Mb, respectively. A total of 32,164 genes was annotated including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Whole genome duplication analyses revealed three putative events, which together with local tandem duplication events, contributed to gene family expa, American beautyberransion of terpene synthases. Kolavenyl diphosphate is a gateway to many of <em>C. americana</em>'s bioactive terpenoids; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with <em>Tectona grandis</em> L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 <em>C. americana</em> syntelogs. Conclusions: Access to the <em>C. americana</em> genome provides a roadmap for rapid discovery of genes encoding plant-derived agrichemicals and a key resource to understand the evolution of chemical diversity in Lamiaceae. </p> <p> </p>
Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade
ABSTRACTSatellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here we use high-quality genome assemblies to study evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 gm/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spreads by inserting into existing clusters of the older, more abundant 1.688 satellite, in events that were likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher-order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.
Construction of a chromosome-scale long-read reference genome assembly for potato
<p><span><strong>Background:</strong> Worldwide, the cultivated potato, <i>Solanum tuberosum </i>L<i>.</i>, is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. <i>tuberosum </i>Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost. </span></p> <p><span><strong>Findings: </strong>Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %) of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length cDNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared to the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the numbersof contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. </span></p> <p><span><strong>Conclusions: </strong>Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.</span></p>
ScienceDex guides
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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.