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345 results for “Sex chromosome”
Data from: Sex-specific recombination landscape in a species with holocentric chromosomes
<p>Male and female meiosis typically exhibit significant differences in crossover locations along chromosomes. It has been suggested that higher recombination rates at chromosome centers in females counteract centromere-associated meiotic drivers, increasing their chances of segregating into the oocyte rather than to the non-viable polar bodies. Our research, employing the first sex-specific recombination map for an organism lacking defined centromeres revealed parallel recombination landscapes across the sexes, supporting the meiotic drive hypothesis.</p>
Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system
<p><em>Schistosoma mansoni </em>has a diploid genome of approximately 380 MB, organized in 7 pairs of autosomes and 2 sex chromosomes. The original <em>Schistosoma mansoni </em>Genome Project was completed by the Wellcome Sanger Institute in collaboration with The Institute for Genome Research using a Whole Genome Shotgun sequencing strategy. The draft assembly was subsequently improved first by incorporating Illumina reads from a clonal (single-miracidial) infection and more recently by incorporating long PacBio reads, HiC, and optical mapping data.</p> <p>Associated manuscript can be found at https://www.biorxiv.org/content/10.1101/2021.08.13.456314v1</p>
Images of article "Sexy ways: the methodical approaches to study plant sex chromosomes"
<p><strong>Figure 1. </strong>Schematic diagram of sex chromosome evolution in dioecious plants. Species are shown according to their level of sex chromosome differentiation and Y chromosome asynapsis. In<em> S. oleracea, A. officinalis</em> and <em>C. papaya</em>, the sex chromosomes are mostly homomorphic with recently formed non-recombining regions (region with suppressed recombination). The non recombining region is largely extended almost to entire chromosomal length in species with heteromorphic sex chromosomes, namely in <em>S. latifolia, R. hastatulus</em> (XY cytotype), <em>R. acetosa, H. lupulus, H. japonicus </em>and<em> M. polymorpha</em>. The position of the centromere, the PAR length and the ratio between X and Y is illustrative. </p> <p><strong>Figure 2.</strong> Laser microdissection as a tool to reduce genome complexity. Sex chromosomes in metaphase are isolated from plant cells (mostly pollen mother cells or root tips) and subsequently spread on a special microscopic slide covered with the membrane. After microdissection, chromosomes are transferred into a tube and processed to other applications. In case of chromosome sorting, the chromosome suspension is stained with a DNA-specific dye and introduced into a flow chamber. Within this chamber, individual chromosomes interact with a laser beam, and the scattered light and emitted fluorescence are measured. Through this process, a histogram of fluorescence intensity (known as a flow karyotype) is generated. Sorting is accomplished by breaking the liquid stream into droplets and electrically charging the droplets containing the chromosomes of interest.</p> <p><strong>Figure 3.</strong> Cytogenetic tools to study sex chromosome origin and evolution. Cytogenetics nowadays combine genomic tools to study repeat fraction including TEs and satellites (a), design unique barcodes to distinguish particular chromosome or chromosomal domain using chromosome oligo-painting probe design (b), and bioinformatic tools to dissect single chromosomes or genome parts (c). The combination of above methods helps to understand sex chromosome evolution regarding their autosomal origin, chromosomal rearrangements, and Y(W) chromosome differentiation. Arrows represent evolutionary steps during sex chromosome divergence (d). The sex chromosome barcoding allows understanding of meiotic pairing which in turn supports chromosomal fusions and inversion/translocations. To chromosomes belong to species with references, from the top to the bottom as follows: <em>S. latifolia </em>Ogre retroelement (Kubat et al., 2014), <em>R. hastatulus</em> XY cytotype satellite Cl135 (Sacchi et al., 2023, Preprint), <em>S. latifolia</em> PAR oligo-painting probe with the subtelomeric satellite X43.1 and centromeric satellite STAR-C (Bačovský et al., 2020), and the same DNA probes on chromosomes in metaphase I in <em>S. latifolia </em>(Bernasconi et al., 2009; Bačovský et al., 2022). </p> <p><strong>Figure 4.</strong> Methodical strategies to assess the function of sex chromosomes in plants. Experimental assays with polyploids (alternatively aneuploids) represent the classical way to determine the role of individual sex chromosomes (a). These assays with plants of various ploidy levels were usually supported by analyses of deletion lines (plants carrying short-chromosomal <br>deletions or microdeletions) (b) that allowed researchers to identify sex-linked regions involved in sex determination and floral development. Modern assays using reverse genetics, such as CRISPR/Cas9, virus-induced gene silencing (VIGS) or peptide treatment of shoot apical meristem (c) provide direct evidence of the gene function and its contribution to the development <br>of reproductive organs. Parasite infected (d) or chemically induced (e) hermaphrodites from either female or male individuals, e.g. in <em>Silene</em> or kaki, let to the identification of key mechanisms and genes that regulate sexual phenotypes, and to understand the regulatory networks leading to separate sexes. </p>
A comprehensive catalog of exact short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of exact repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,233,959 TR intervals, covering 0.783306% (24.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark
Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species.
Sex chromosomes and hormones independently influence healthy brain development but act similarly after cranial radiation
<h2><strong>Description</strong></h2> <p>Biological sex influences prevalence of developmental disorders through sex hormones and sex chromosomes. However, our understanding of their impacts in neurodevelopment and response to injury remains limited. In this project, we use high resolution magnetic resonance imaging (MRI) to investigate the four core genotype mouse model (FCG) that separates the influences of sex hormones and sex chromosomes during normal brain development and after cranial radiation therapy. </p> <p>Sex differences are attributed to either sex hormones or sex chromosomes. This can be distinguished by the FCG model which decouples the sex determining region (SRY) from the Y chromosome by moving SRY onto an autosome. This gives us four core sex genotypes: XX NULL, XY NULL, XX SRY, and XY SRY.</p> <p>This dataset represents the <em>most comprehensive mouse brain imaging study</em> employing the FCG model to date with 5 timepoints (P14, P23, P42, P63, P98), Ccl2 wildtype (+/+) and knockouts (-/-), irradiation (7Gy) and sham (0Gy) mice. All in all, a total of <strong>1071 images</strong>! The results presented here is published in PNAS.</p> <p>In vivo MRI scans were obtained using a 7-T MRI scanner (Bruker BioSpin, Ettlingen, Germany) equipped with four cryocoils for simultaneous imaging of four mice. The scans were performed with the following settings: T1-weighted, 3D-gradient echo sequence, 75μm isotropic resolution, TR=26ms, TE=8.25ms, flip angle=26°, field of view=25×22×22mm, and matrix size=334×294×294.</p> <p>All structural MR images are stored in <strong>images.tar.gz</strong>. Images were segmented and registered using an automated pipeline which are stored in <strong>labels.tar.gz</strong>. The consensus average and labels are <strong>final_average.mnc </strong>and <strong>final_labels.mnc</strong>, respectively. Extracted structure volumes alongside the metadata are included in <strong>df_micevolumes.csv</strong>. Structural MRIs are in MINC format and the <strong>readme.txt</strong> provides further information on this dataset. </p> <p>The authors express their sincere gratitude for the research funding recieved from the Canadian Institutes of Health Research (158622, 168037) and the Ontario Institute for Cancer Research (IA-024) with funding from the Government of Ontario and Restracomp from the SIckKids Research Training Centre.</p> <p><strong>Publication</strong>: https://www.pnas.org/doi/10.1073/pnas.2404042121</p> <h2><strong>Code/Software </strong></h2> <p><strong>MINC</strong><br>https://www.bic.mni.mcgill.ca/ServicesSoftware/MINC</p> <p><strong>RMINC</strong><br>https://github.com/Mouse-Imaging-Centre/RMINC</p> <p><strong>PydPiper</strong><br>https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.19.1</p>
Data from: Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry
<p>Abstract: When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex determining region (SDR) of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome scale assembly of a female (ZW) <em>Fragaria chiloensis</em> plant carrying the youngest and largest of the known SDR on the W in strawberries. We fully characterized the previously incomplete SDR, confirming its gene content, genomic location and evolutionary history. Resolution of gaps in the previous characterization of the SDR added 10 kbp of sequence including a non-canonical LTR-retrotransposon; whereas the Z sequence revealed a <em>Harbinger</em> transposable element adjoining the SDR insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.</p> <p>Repository content: data (sequence alignments, phylogenetic trees, genome assembly, and vcf files) and scripts associated with the manuscript "Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry"</p>
Supplementary material 2 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
Supplementary Figure S. (doi: 10.3897/CompCytogen.v8i1.6716.app2) File format: Microsoft Word file (doc).:
A comprehensive catalog of approxiamte short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of approximate repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,656,159 TR intervals, covering 1.107653% (34.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
Fig. 65 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 65. Evolution of carnivory inferred from our optimization of the carnivory character of Ferrarezi and Gimenez (1996: table 1; see our table 8) on our strict consensus tree from the character congruence analysis. The ''uncertain'' states for Phyllostomus and Tonatia are due to taxonomic polymorphism.
Fig. 64 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 64. Evolution of different types of nectarivory inferred from our optimization of the nectarivory character of Ferrarezi and Gimenez (1996: table 1; see our table 8) on our strict consensus tree from the character congruence analysis. Note that the nectarivory character, as defined by Ferrarezi and Gimenez (1996) includes the consumption of pollen and petals. To prevent an equivocal reconstruction for the base of the clade that includes all phyllostomids except desmodontines, we examined trees in which the position of Brachyphylla was resolved and fixed the node at the base of the clade that includes all phyllostomids except desmodontines with the state that occurred under the two alternative placements for this genus.
Fig. 63 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 63. Evolution of different types of frugivory inferred from our optimization of the frugivory character of Ferrarezi and Gimenez (1996: table 1; see our table 8) on our strict consensus tree from the character congruence analysis. To prevent an equivocal reconstruction for the base of the clade that includes all phyllostomids except desmodontines, we examined trees in which the position of Brachyphylla was resolved and fixed the node at the base of the clade that includes all phyllostomids except desmodontines with the state that occurred under the two alternative placements for this genus.
Fig. 62 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 62. Evolution of different types of insectivory (see text for description of character states) inferred from our optimization of the insectivory character of Ferrarezi and Gimenez (1996: table 1; see our table 8) on our strict consensus tree from the character congruence analysis. We inferred the state at the root with reference to a phylogeny of Microchiroptera (Simmons, 1998). The equivocal optimizations for Phyllostomidae and Vampyrini are due to differences in interpretation of the character under ACCTRAN or DELTRAN. The ''uncertain'' state for Noctilio is due to taxonomic polymorphism (see table 8).
Fig. 61 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 61. Tree used by Ferrarezi and Gimenez (1996; redrawn from fig. 4) with their feedinghabits character optimized on the topology. This character was ordered such that predominant insectivory evolved from strict insectivory; predominant carnivory, predominant frugivory, or sanguivory evolved from predominant insectivory; and predominant nectarivory or strict frugivory evolved from predominant frugivory.
Fig. 60 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 60. Evolution of the labial horseshoe inferred from optimization of character 25 on the strict consensus tree from our character congruence analysis. The morphology of the thickened labial horseshoe (character 27) is also indicated: asterisks indicate taxa with a Vshaped labial projection; a single cross indicates taxa in which all individuals have a Vshaped notch; a double cross indicates taxa in which some individuals have a Vshaped notch. The state for Centurio is not indicated because we scored this taxon ''?'' for all characters related to the noseleaf (see character 18).
Fig. 59 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 59. Evolution of the lateral horseshoe inferred from optimization of character 24 on the strict consensus tree from our character congruence analysis. The equivocal reconstruction for the evolution of a ''partly free edge'' is due to the missing data for Scleronycteris.
Fig. 58 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 58. Evolution of the internarial structures inferred from optimization of character 24 on the strict consensus tree from our character congruence analysis. The equivocal reconstruction within Hirsutaglossa is due to alternative interpretations under ACCTRAN and DELTRAN. Note that ''polymorphic'' indicates that some individuals in a species have a ridge or papillae, whereas others do not.
Fig. 57 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 57. Evolution of length of the central rib inferred from optimization of character 21 on the strict consensus tree from our character congruence analysis. The equivocal reconstruction for the base of the clade including phyllostomines and nullicaudans is due to alternative interpretations under ACCT RAN and DELTRAN. The reconstruction for Centurio is equivocal due to missing data (see character 18). See text for discussion.
Fig. 56 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 56. Evolution of spear length and spear tip shape inferred from the optimization of characters 19 and 20, respectively, on the strict consensus tree from our character congruence analysis. Optimization of spear length A. with Brachyphylla as the sister taxon of Hirsutaglossa, Phyllostominae, and Nullicauda. The equivocal reconstruction beginning with the last common ancestor the clade including Hirsutaglossa, Phyllostominae, and Nullicauda is due to alternative optimizations under ACCTRAN and DELTRAN. B. with Brachyphylla as the sister taxon of Phyllostominae and Nullicauda. Optimizations of spear tip shape C. with Brachyphylla as the sister taxon of Hirsutaglossa, Phyllostominae, and Nullicauda, and D. with Brachyphylla as the sister taxon of Phyllostominae and Nullicauda. The equivocal reconstruction beginning with the last common ancestor of Phyllostomidae is due to alternative reconstructions under ACCTRAN and DELTRAN.
Fig. 54 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 54. Evolution of the number of interramal vibrissae inferred from optimization of character 13 on the strict consensus tree from our character congruence analysis. The equivocal reconstruction for Scleronycteris is due to missing data, while in Phyllostomus it is caused by taxonomic polymorphism. The equivocal reconstruction of this character in Vampyrini is due to the occurence of taxonomic polymorphism in Tonatia; there are two possible resolutions of this character in this clade under ACCT
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