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3,457 results for “chromosomes”
Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
<p><span><span><span><span><span><span><span><span><span><span><span>The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon. Here, we explain this association by elucidating a mutational cascade, downstream of <a>th</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>e single cell division error of chromosome bridge formation, that rapidly generates extreme genomic complexity. We show that actomyosin forces are required for initial bridge breakage and mutagenesis, following which chromothripsis accumulates with aberrant interphase replication of bridge DNA. This is then followed by an unexpected burst of DNA replication in the next mitosis, generating extensive DNA damage. During this second cell division, broken bridge chromosomes frequently mis-segregate and form micronuclei, promoting additional chromothripsis. We <a>fu</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>rther show that this mutational cascade generates the continuing evolution and sub-clonal heterogeneity characteristic of many human cancers.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We found that perennials likely possess the derived orientation of the inversion. In addition, this perennial orientation occurs in a second perennial species, M. decorus, where it is strongly associated with life-history differences between co-occurring M. decorus and annual M. guttatus. One prediction of the recombination suppression hypothesis is that loci contributing to local adaptation will predate the inversion. To test whether the loci influencing perenniality pre-date this inversion, we mapped QTLs for life history traits that differ between annual M. guttatus and a more distantly related, collinear perennial species, M. tilingii. Consistent with the recombination suppression hypothesis we found that this region is associated with life-history in the absence of the inversion, and this association can be broken into at least two QTLs. However, the absolute phenotypic effect of the LG8 inversion region on life-history is weaker in M. tilingii than in perennials which possess the inversion. Thus, while we find support for the recombination suppression hypothesis, the contribution of this inversion to life history divergence in this group is likely complex.
Data from: Genetic responsiveness of African buffalo to environmental stressors: a role for epigenetics in balancing autosomal and sex chromosome interactions?
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distorter-suppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequency-dependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.
Data from: Mapping reduced introgression loci to the X chromosome of the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus
The genomic architecture of barriers to gene exchange during the speciation process is poorly understood. The genomic islands model suggests that loci associated with barriers to gene exchange prevent introgression of nearby genomic regions via linkage disequilibrium. But few analyses of the actual genomic location of non-introgressing loci in closely related species exist. In a previous study Maroja et al. showed that in the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus, 50 non-introgressing loci are localized on two autosomal regions and the X chromosome, but they were not able to map the loci along the X chromosome because they used a male informative cross. Here, we localize the introgressing and non-introgressing loci on the X chromosome and reveal that all X-linked non-introgressing loci are restricted to a 50-cM region with 10 of these loci mapped to a single location. We discuss the implications of this finding to speciation.
Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype
<p>Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (<em>Helianthus petiolaris</em>) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and non-dune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within arrangements, consistent with the behavior of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions co-locate with previously described "islands of differentiation," and appear to play an important role in adaptive divergence and incipient speciation within <em>H. petiolaris</em>.</p>
Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution
<p>Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower<i>,</i> <i>Helianthus</i> <i>petiolaris</i> ssp. <i>petiolaris</i> and <i>H. petiolaris</i> ssp. <i>fallax.</i> Using <i>syntR</i>, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years – a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that <i>Helianthus</i> has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.</p>
The Greeks in the West - Y chromosome dataset
<p>This dataset contains data of 20 microsatellites and 59 Y chromosome SNPs regarding 23 newly genotyped population from Italy, Greece, Croatia, Turkey and Albania. </p>
Figure 1. - Mitotic metaphases, karyograms and idiogram of Euterpe species with 2n=36 chromosomes. Euterpeedulis (A–B), Euterpeoleracea (C-D) and Euterpeprecatoria (E–F). Arrows indicate secondary constrictions. Semi-reticulate interphase nuclei of Euterpeedulis (G), Euterpeoleracea (H) and Euterpeprecatoria (I). Bar: 10 µm.
Figure 1. - Mitotic metaphases, karyograms and idiogram of Euterpe species with 2n=36 chromosomes. Euterpeedulis (A–B), Euterpeoleracea (C-D) and Euterpeprecatoria (E–F). Arrows indicate secondary constrictions. Semi-reticulate interphase nuclei of Euterpeedulis (G), Euterpeoleracea (H) and Euterpeprecatoria (I). Bar: 10 µm.
A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
<p>Quinoa (<em>Chenopodium</em> <em>quinoa</em> Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for three accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we used in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned 1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds. The genome was annotated with 54,499 protein-coding genes, 97% of which were located on the 18 largest scaffolds. We also produced an updated genome assembly for the B-genome diploid <em>C. suecicum</em> and used it, together with the A-genome diploid<em> C. pallidicaule</em>, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.20%, 48.61%, and 57.91% of the quinoa, <em>C. pallidicaule</em>, and <em>C. suecicum</em> genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.</p>
Data supporting: Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa
<p>The genus <em>Acacia</em> is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many <em>Acacia</em> species are capable of developing leaves of both bifacial and unifacial morphology. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. Here we identify an accession of <em>Acacia crassicarpa</em> with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone and using comparative analyses confirm a whole genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in <em>Acacia</em>.</p>
Supplemental Movie Files for "Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis" by Chriss et al.
<p>This set of Supplemental Information contains two movies made from the simulations from the model developed in the manuscript "<strong>Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis</strong>" by A. Chriss, G. V. Börner, and S. D. Ryan. </p> <p> </p> <p>Supplemental Movie S1: <strong>WT Chromosome Trajectories during Prophase I. </strong>The first file "movie_WT..." contains the file for the results of simulations for the wild-type chromosomes and the exact parameter values can be found in Table 1 of the manuscript. The movie shows one realization of the agent-based model. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S2: <strong>WT Chromosome Trajectories during Prophase I with active dumbbell model. </strong> The second file "movie<em>WT</em>_activedumbbell..." contains the file for the results of the simulations for the modeling of chromosomes as active dumbbells (from polymers) to allow for the study of the effects of elongation, orientation, and flexibility. The movie shows one realization of the agent-based active dumbbell model which is closer to modeling a chromosome as a polymer. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii, but are allowed to change in time as the two beads expand and contract. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S3: <strong><em>spo11</em> hypomorph (30% WT DSB levels) Chromosome Trajectories during Prophase I (parameters from Fig 7B)</strong>. The third file "movie_spo11..." contains the file for the results of the simulations for the spo-11 hypomorph and the associated parameter values can be found in Table 1 of the manuscript. The movie depicts one realization of the agent-based model for the {\it spo11} hypomorphic mutant. The simulation movie covers the homology search process from <em>t = 3h</em> to <em>t = 9h</em> where mutant <em>spo11</em> is associated with a weaker attractive and repulsive force (e.g., reduction to 77% of WT values). True chromosome lengths are incorporated and scale the relevant interaction radii. Matching colors correspond to homologous pairs. The radii represent the homologous attractive and the non-homologous repulsive region. Note that the reduction in interaction strength delays homologous pairing consistent with experimental observations in [13]. </p> <p> </p> <p> </p> <p>The codes that generated these movies were written in Matlab and freely available via GitHub: <a href="https://github.com/sdryan/ChromosomeDynamicsProphase1">https://github.com/sdryan/ChromosomeDynamicsProphase1</a></p> <p> </p> <p>For questions please contact the corresponding authors: G. Valentin Börner <a href="mailto:g.boerner@csuohio.edu">g.boerner@csuohio.edu</a> (Biology) or Shawn D. Ryan <a href="mailto:s.d.ryan@csuohio.edu">s.d.ryan@csuohio.edu</a> (Math).</p>
mRatBN7.2 chromosomal regions containing misassembled segments
<p>This file contains regions of the mRatBN7.2 that contain misassembled segments. The code for generating these results are available in github:</p> <p>https://github.com/hanyoupan/rat-manuscript/tree/main/5_IdentifyingMisAssembledSegments</p>
Sex-biased gene content associates with sex chromosome turnover in Danaini butterflies
<p>Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here we investigate the evolutionary origin of the previously reported <em>Danaus</em> neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of <em>Tirumala septentrionis</em> (subtribe Danaina), <em>Ideopsis similis</em> (Amaurina), <em>Idea leuconoe</em> (Euploeina), and <em>Lycorea halia</em> (Itunina) and identified their Z-linked scaffolds. We found that the <em>Danaus </em>neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the <em>Melitaea cinxia</em> chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina, and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in <em>I. similis</em> and independent fusion occurred between the ancestral Z chromosome and McChr12 in <em>L. halia</em>. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analyzing the genomic distribution of sex-biased genes in <em>I. leuconoe</em> and <em>L. halia</em>. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both <em>I. leuconoe</em> and <em>L. halia</em> appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z is variable across tissues and species.</p>
Data from: Male mouse recombination maps for each autosome identified by chromosome painting
<p>Linkage maps constructed from genetic analysis of gene order and crossover frequency provide few clues to the basis of the genomewide distribution of meiotic recombination, such as chromosome structure, that influences meiotic recombination. To bridge this gap, we have generated the first cytological recombination map that identifies individual autosomes in the male mouse. We prepared meiotic chromosome (synaptonemal complex [SC]) spreads from 110 mouse spermatocytes, identified each autosome by multicolor fluorescence in situ hybridization of chromosome- specific DNA libraries, and mapped 12,000 sites of recombination along individual autosomes, using immunolocalization of MLH1, a mismatch repair protein that marks crossover sites. We show that SC length is strongly correlated with crossover frequency and distribution. Although the length of most SCs corresponds to that predicted from their mitotic chromosome length rank, several SCs are longer or shorter than expected, with corresponding increases and decreases in MLH1 frequency. Although all bivalents share certain general recombination features, such as few crossovers near the centromeres and a high rate of distal recombination, individual bivalents have unique patterns of crossover distribution along their length. In addition to SC length, other, as-yet-unidentified, factors influence crossover distribution leading to hot regions on individual chromosomes, with recombination frequencies as much as six times higher than average, as well as cold spots with no recombination. By reprobing the SC spreads with genetically mapped BACs, we demonstrate a robust strategy for integrating genetic linkage and physical contig maps with mitotic and meiotic chromosome structure.</p>
Data from: Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii
<p>Wheat (<em>Triticum aestivum</em>) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Wheat's wild relative species provide a hugely untapped reservoir of genetic diversity for wheat improvement. <em>Triticum timopheevii</em> (2n = 4x = 28) is a tetraploid wheat wild relative species containing the A<sup>t</sup> and G genomes that has been exploited in many wheat pre-breeding programmes over the last few decades. In this study, we report the generation of a chromosome-scale reference genome assembly of <em>T. timopheevii</em> accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The total assembly size was 9.35 Gb with a contig N50 of 42.4 Mb. In total, 166,325 gene models were predicted. Comparative genome analysis confirmed previously known chromosomal translocations and indicated new chromosome rearrangements. Analysis of the genomic distribution of DNA methylation showed that the G genome had on average more methylated bases than the A<sup>t</sup> genome. The G genome was also more closely related to the<em> </em>S genome of <em>Aegilops speltoides</em> than to the B genome of hexaploid or tetraploid wheat. In summary, the <em>T. timopheevii</em> genome assembly provides a valuable resource for genome-informed discovery and cloning of agronomically important genes for future food security.</p>
Data: Chromosomal inversions and the demography of speciation in Drosophila montana and Drosophila flavomontana
<p>Chromosome-level genome assemblies of Drosophila montana and Drosophila flavomontana that are associated with the publication "Chromosomal inversions and the demography of speciation in Drosophila montana and Drosophila flavomontana" by Poikela et al. (2024).</p> <p>Dmontana_chromosomes = only D. montana scaffolds assigned to chromosomes</p> <p>Dmontana_all_regions = all genomic D. montana regions</p> <p>Dflavomontana_chromosomes = only D. flavomontana scaffolds assigned to chromosomes</p> <p>Dflavomontana_all_regions = all genomic D. flavomontana regions</p>
Phylogenetics, taxonomy, and chromosome number analysis of Sanvitalia (Asteraceae-Heliantheae-Zinniinae)
<p>We collected molecular sequence data from the nuclear ribosomal ITS region and three plastid loci from multiple individuals of each species of Sanvitalia and additional members of the Zinniinae to create phylogenetic trees and study the evolutionary history of the clade. The alignments used for these trees is included here.</p>
Striking variation in chromosome structure within Musa acuminata and its diploid cultivars
<p>The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, <em>Musa acuminata</em> and <em>Musa balbisiana</em>. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility of edible clones and differences in the chromosome structure among <em>M. acuminata</em> subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo painting we investigated large chromosomal rearrangements in a set of wild <em>M. acuminata</em> subspecies and cultivars that originated by natural crosses. Additionally, we analyzed chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and wild <em>M. acuminata </em>'Calcutta 4' genotype. Analysis of chromosome structure within <em>M. acuminata</em> revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing, which enabled to identify the contribution of parental subgenomes to the diploid hybrid clones. Balanced presence of both parental genomes was revealed in all F1 hybrids with the exception of one clone, which contained only Mchare specific SNPs, and thus most probably originated from an unreduced diploid gamete of Mchare.</p>
Chromosomal instability degrades developmental phenotypes essential for anti-GD2 immunotherapy outcomes in high-risk neuroblastoma
<p>Childhood Cancer Data Initiative (CCDI)<br>dbGaP Study Accession: phs002431</p>
Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.
<p><em>Alopecurus aequalis</em> is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of <em>A. aequalis</em> with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of <em>A. aequalis</em> is more similar to <em>Hordeum vulgare </em>rather than the more closely related <em>Alopecurus myosuroides</em>. The datasets provided here are the assembly FASTA file (lpAloAequ1.1.prim.cur.20230912.fasta.gz), the high-confidence protein-coding genes (Alaeq_EIv0.2.release_HC_genes.gff3.gz) and the full annotation which includes both low and high confidence features of all biotypes (Alaeq_EIv0.2.release.gff3.gz) </p>
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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.