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3,457 results for “chromosomes”
Heterogeneous evolution of sex chromosomes in the torrent frog genus Amolops
<p>In sharp contrast with birds and mammals, sex chromosomes have been described as homomorphic in cold-blooded vertebrates. This sex-chromosome homomorphy has been suggested to result from high turnovers when they are often observed across deeply diverged clades. However, little is known about the tempo and mode of sex chromosome evolution among most closely related species. Here, we examine patterns of sex chromosome evolution among nine species of the torrent frog genus <em>Amolops</em>. Through the analysis of male and female GBS and RAD-seq from 182 individuals and of PCR verification for 176 individuals, we identify signatures of sex chromosomes involving two pairs of chromosomes. We find that the sex-chromosome homomorphy results from both turnover and X–Y recombination in the <em>Amolops</em> species, simultaneously exhibiting heterogeneous evolution on homologous and non-homologous sex chromosomes. The lower turnover rate of non-homologous sex chromosomes exists in these torrent frogs, whereas the ongoing X–Y recombination in homologous sex chromosomes would act as an indispensable force to prevent the sex chromosomes from differentiations. </p>
A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax
<p>The New World Screwworm, <em>Cochliomyia hominivorax</em> (Calliphoridae), is the most important myiasis-causing species in America. Screwworm myiasis is a zoonosis that can cause severe lesions in livestock, domesticated and wild animals, and occasionally in people. Beyond the sanitary problems associated with this species, these infestations negatively impact economic sectors, such as the cattle industry.</p> <p>Here, we present a chromosome-scale assembly of <em>C</em>. <em>hominivorax</em>'s genome, organized in 6 chromosome-length and 515 unplaced scaffolds spanning 534 Mb. There was a clear correspondence between the <em>D</em>. <em>melanogaster</em> linkage groups A-E and the chromosomal-scale scaffolds. Chromosome Quotient (CQ) analysis identified a single scaffold from the X chromosome that contains most of the orthologs of genes that are on the <em>D</em>. <em>melanogaster</em> fourth chromosome (linkage group F or dot chromosome). CQ analysis also identified potential X and Y unplaced scaffolds and genes. Y-linkage for selected regions was confirmed by PCR with male and female DNA. Some of the long chromosome-scale scaffolds include Y-linked sequences, suggesting misassembly of these regions. These resources will provide a basis for future studies aiming at understanding the biology and evolution of this devastating obligate parasite.</p>
Supplementary material 1 from: Steinberg E, Nieves M, Mudry M (2014) Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). Comparative Cytogenetics 8(1): 43-69. https://doi.org/10.3897/compcytogen.v8i1.6716
Data matrix. (doi: 10.3897/CompCytogen.v8i1.6716.app1) File format: Microsoft Word file (doc).:
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
<p><span>Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for <em>Phytophthora sojae</em>, <em>Globisporangium ultimum</em>, <em>Pythium oligandrum</em>, and <em>G. spinosum</em>. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with <em>Copia</em>-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in <em>P. sojae</em>. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.</span></p>
Chromosome-level assembly and annotation of Lates japonicus
<p>It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes (<em>N</em><sub>e</sub>s) and low levels of genetic polymorphisms. To understand the importance of genome-wide genetic diversity for the long-term persistence of natural populations in threatened species, we determined the whole genome sequences of akame (<em>Lates japonicus</em>), which is considered to have survived a long time with extremely low genetic variations. Genome-wide single nucleotide variant heterozygosity in akame was estimated to be 3.3–3.4 × 10<sup>-4</sup> /bp, one of the smallest values in teleost fishes. Analysis of demographic history inferred that the <em>N</em><sub>e</sub> in akame was around 1,000 from 30,000 years ago to the recent past. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions containing genes involved in immunity, synaptic development, and olfactory sensory systems have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential in fluctuating environments. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, indicating that adaptive evolution to the temperate waters has occurred after the speciation of akame and its close relative, barramundi (<em>L. calcarifer</em>). Our results indicated that the functional genetic diversity in akame likely contributed to avoiding the harmful effects of the reduced population size, despite the increased genetic load in this species.</p>
Data from: The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals
<p>The XX/XY sex chromosome system is deeply conserved in therian mammals, as is the role of <em>Sry</em> in testis determination, giving the impression of stasis relative to other taxa. However, the long tradition of cytogenetic studies in mammals documents sex chromosome karyotypes that break this norm in myriad ways, ranging from fusions between sex chromosomes and autosomes to Y chromosome loss. Evolutionary conflict, in the form of sexual antagonism or meiotic drive, is the primary predicted driver of sex chromosome transformation and turnover. Yet conflict-based hypotheses are less considered in mammals, perhaps because of the perceived stability of the sex chromosome system. To address this gap, we catalogue and characterize all described sex chromosome variants in mammals, test for family-specific rates of accumulation, and consider the role of conflict between the sexes or within the genome in the evolution of these systems. We identify 152 species with sex chromosomes that differ from the ancestral state and find evidence for different rates of ancestral to derived transitions among families. Sex chromosome-autosome fusions account for 80% of all variants whereas documented sex chromosome fissions are limited to three species. We propose that meiotic drive and drive suppression provide viable explanations for the evolution of many of these variant systems, particularly those involving autosomal fusions. We highlight taxa particularly worthy of further study and provide experimental predictions for testing the role of conflict and its alternatives in generating observed sex chromosome diversity.</p>
Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure
<p>Orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, can be seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the importance of genome organization to gene regulatory landscapes. Here, we report a unique pattern of genome evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, including phylogenetic reconstruction and orthologous gene mapping, we reconstruct the chromosomal evolutionary history of five bryozoans. We infer the ancestral bryozoan genome organization and identify multiple ancient chromosome fusions followed by gene mixing, leading to the near-complete loss of bilaterian linkage groups. A second wave of rearrangements, including chromosome fission, occurred independently in two bryozoan classes, further shuffling bryozoan genomes. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional yet highly debated Lophophorata hypothesis. Finally, we show that chromosome fusion and fission processes led to the separation of bryozoan Hox clusters. Our findings demonstrate that the canonical bilaterian genome structure has been lost across an entire phylum, reveal that linkage group fission can occur very frequently in specific lineages, and provide a powerful source of phylogenetic information.</p>
The history of chromosomal instability in genome doubled tumors : Data release
<p>Released data for '<em>The history of chromosomal instability in genome doubled tumors</em>'.</p>
Fig. 2 in Medicago Falcata L. In Estonia: Chromosomal And Morphologicalvariability, Distribution And Vulnerability Oftaxa
Fig. 2. Dendrogram of M. falcata (Ward's algorithm), measured characters
Data from: Rewinding the ratchet: Rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence
<p>Natural selection is less efficient in the absence of recombination. As a result, non-recombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, <em>Melanargia ines</em>, where a Z-autosome fusion has turned the homologous autosome into a non-recombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of <em>M. ines</em>, and that they arose around the time when this population split from North-African populations, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop codons and frameshift mutations, and reduced gene expression compared to the neo-Z chromosome. Surprisingly, we identified two regions of 1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.</p>
Data and Codes for "Long-Range Repulsion Between Chromosomes in Mammalian Oocyte Spindles"
<p>Complete source data and analysis codes for the paper "Long-Range Repulsion Between Chromosomes in Mammalian Oocyte Spindles" by Colm P Kelleher, Yash P Rana, and Daniel J Needleman</p> <p> </p> <p>Updates available at https://osf.io/p9t7z/</p>
Chromosome-level genome assembly of Cyamophila willieti (Hemiptera: Psyllidae)
Open the record for dataset details and reuse information.
Chromosome-level genome assemblies of sunflower oilseed and confectionery cultivars
<p>In this study, we obtained high-quality genomes of two cultivar representatives of oil and confectionery common sunflower (Helianthus annuus L.) lineages in China at the chromosome level using the PacBio Revio system Circular Consensus Sequencing and high-throughput chromatin conformation capture (Hi-C) scaffolding sequencing technologies. OXS is an inbred oil-type sunflower line with high kernel rate (74.5% kernels), contains 42.9% oil and fat. It is highly susceptible to Verticillium wilt and moderately susceptible to several other diseases. YDS is an inbred non-oil line with high plant height (180-220 cm) and large plump seeds (19.23 grams per 100 seeds). The genome assembly of OXS, spans 3.03 Gb, with 99.58% of sequences anchored to 17 chromosomes and a contig N50 length of 154 Mb. Similarly, the assembly size of YDS, is 3.02 Gb, with 99.40% of sequences mapped to 17 chromosomes and a contig N50 length of 153 Mb. The gene completeness of BUSCO reached 98.2% for OXS and 98.4% for YDS, while the LTR Assembly Index (LAI) stood at 24.73 and 25.85 for OXS and YDS, respectively. A comparative genomics approach identified 6,535 (OXS) and 6,498 (YDS) gene families that have evolved rapidly and are associated with substance synthesis, cell growth, grain weight, and protective mechanisms against biotic and abiotic stresses. We discovered that the YDS genome assembly shows high collinearity with the OXS assembly, apart from three significant inversions on chromosomes 7 and 17. We also identified 15,056 large deletions and insertions between the OXS and YDS assemblies. The publication of these genomes has greatly contributed to the improvement of genetic breeding by integrating internal genetic and external environmental factors in Helianthus annuus L. crops.</p>
Test data for C-QTL analysis of barley Recombinant Chromosome Substitution Lines
<p>This data shows the testing of C-QTL approach to visualise the influence of ensembles of groups of genetic markers on plant traits from a selection of Recombinant Chromosome Substitution Lines. The analysis was performed on of 29 genotypes and two traits: Heading Date and plant height. For heading date, the two major QTLs on 2H and 7H associated with heading date using the REML approach (de la Fuente Canto 2016) are also detected using the CQTL analysis, getting the highest 'rank' or score with this approach. Similarly, marker main effect for plant height at the region of the sdw1 seems to be detected with the CQTL analysis.</p>
Evolutionary mechanisms of varying chromosome numbers in the radiation of Erebia butterflies
<p>This is the dataset for the study with the same title published at MDPI Genes (please see the paper for all details).</p> <p>To test for a phylogenetic signal of varying chromosome numbers in Erebia butterflies (Lucek submitted), I reconstructed a phylogeny using a subset of Peña et al. Biol J Linn Soc 2016 for which chromosome numbers were available. Data for an additional 5 species was taken from GenBank. Chromosome numbers used are included.<br> The final alignment comprised sequence data for four genes: 620 bp of the mitochondrial cytochrome oxidase subunit I (COI), 598 bp of the nuclear glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 565 bp of the nuclear ribosomal protein S5 (RpS5) and 343 bp of the nuclear wingless gene.</p> <p>I used PartitionFinder 2 (Lanfear et al. Mol Biol Evol 2017) to infer the best partition scheme and associated substitution model for each codon position and gene. The output of PartitionFinder is provided in the data file. The resulting best partitioning scheme for the Bayesian inference is given in each nexus file. For the maximum likelihood (ML) based phylogeny I used the GTR model with invariant sites and gamma correction (GTR+I+G) in RAXML 8.2.8 (Stamatakis, Bioinformatics 2014) with the corresponding partition scheme from PartitionFinder. I further used 1000 bootstrap replicates to assess significance. I ran RAXML for the dataset comprising either all four genes, the mitochondrial COI gene only or the three nuclear genes. In the latter case, data was only available for 35 taxa. I conducted the Bayesian analysis in MrBayes 3.2.2 (Ronquist et al. Syst Biol 2012) for either dataset using in each case, 5’000’000 generations with four chains – three heated and one cold. Trees were sampled every 1’000 generations.<br> Provided are the input and output files of MrBayes and RAXML for all genes combined (subfolder all), the mitochondrial COI gene only (subfolder mtdna) or the three nuclear genes (subfolder nuclear).</p>
Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics
<p>Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics</p>
Supplemental files for the manuscript "Chromosome assembly of large and complex genomes using multiple references"
<p>This archive contains supplemental files for the manuscipt: "Chromosome assembly of large and complex genomes using multiple references".</p> <p>It contains assemblies generated by Ragout and RACA as well as evaluation scripts that were used in our analysis.</p> <p>Each subdirectory contains an additional README file with details.</p> <p>Please note that some intermediate files were deleted in the interest of saving space. If you need access to those files or having issues with reproducing our results, don't hesitate to contact Mihkail Kolmogorov: fenderglass@gmail.com</p>
Figure 4 in Comparison of the chromosome banding patterns in Dryomys laniger and D. nitedula from Turkey
Figure 4. Silver stained karyotypes of Dryomys laniger (1) and Dryomys nitedula (2).
Figure 3. C in Comparison of the chromosome banding patterns in Dryomys laniger and D. nitedula from Turkey
Figure 3. C-banded karyotypes of Dryomys laniger (1) and Dryomys nitedula (2).
Figure 2 in Comparison of the chromosome banding patterns in three species of social voles (Microtus irani karamani, M. schidlovskii, M. anatolicus) from Turkey
Figure 2. Standard karyotypes of M. irani karamani (1), M. schidlovskii (2), and M. anatolicus (3).
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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.