Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1059008 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27594100_1.fastq.gz | Fastqsanger.gz | |||
| SRR27594100_2.fastq.gz | Fastqsanger.gz | |||
| SRR27594101_1.fastq.gz | Fastqsanger.gz | |||
| SRR27594088_1.fastq.gz | Fastqsanger.gz | |||
| SRR27594088_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only ~10 MYA and is a promising model organism to study sex chromosome evolution in plants. Previous work suggests that S. latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is undergoing degeneration as in animal sex chromosomes. However, this work has been limited by the paucity of sex-linked genes available. Here, we used 35 Gb of RNA-seq data from multiple males (XY) and females (XX) of a S. latifolia inbred line to detect sex-linked SNPs and identified more than 1700 sex-linked contigs (with X-linked and Y-linked alleles). Analyses using known sex-linked and autosomal genes, together with simulations indicate that these newly identified sex-linked contigs are reliable. Using read numbers, we then estimated expression levels of X-linked and Y-linked alleles in males and found an overall trend of reduced expression of Y-linked alleles, consistent with a widespread ongoing degeneration of the S. latifolia Y chromosome. By comparing expression intensities of X-linked alleles in males and females, we found that X-linked allele expression increases as Y-linked allele expression decreases in males, which makes expression of sex-linked contigs similar in both sexes. This phenomenon is known as dosage compensation and has so far only been observed in evolutionary old animal sex chromosome systems. Our results suggest that dosage compensation has evolved in plants and that it can quickly evolve de novo after the origin of sex chromosomes.
2012-08-24 | GSE35563 | GEO
Project description:Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only ~10 MYA and is a promising model organism to study sex chromosome evolution in plants. Previous work suggests that S. latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is undergoing degeneration as in animal sex chromosomes. However, this work has been limited by the paucity of sex-linked genes available. Here, we used 35 Gb of RNA-seq data from multiple males (XY) and females (XX) of a S. latifolia inbred line to detect sex-linked SNPs and identified more than 1700 sex-linked contigs (with X-linked and Y-linked alleles). Analyses using known sex-linked and autosomal genes, together with simulations indicate that these newly identified sex-linked contigs are reliable. Using read numbers, we then estimated expression levels of X-linked and Y-linked alleles in males and found an overall trend of reduced expression of Y-linked alleles, consistent with a widespread ongoing degeneration of the S. latifolia Y chromosome. By comparing expression intensities of X-linked alleles in males and females, we found that X-linked allele expression increases as Y-linked allele expression decreases in males, which makes expression of sex-linked contigs similar in both sexes. This phenomenon is known as dosage compensation and has so far only been observed in evolutionary old animal sex chromosome systems. Our results suggest that dosage compensation has evolved in plants and that it can quickly evolve de novo after the origin of sex chromosomes. 2 Samples (male and female) in triplicates
2012-08-24 | E-GEOD-35563 | biostudies-arrayexpress
Project description:Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes can also facilitate this by directly linking gene expression to sex. Moreover, heteromorphic sex chromosomes often exhibit different gene content, which contributes to sexual dimorphism. Understanding patterns of sex-biased gene expression across organisms is important for gaining insight about the evolution of sexual dimorphism and sex chromosomes. Moreover, studying gene expression in species with recently established sex chromosomes can help understand the evolutionary dynamics of gene loss and dosage compensation. The threespine stickleback is known for its strong sexual dimorphism, especially during the reproductive period. Sex is determined by a young XY sex chromosome pair with three non-recombining regions that have started to degenerate. Using the high multiplexing capability of 3′ QuantSeq to sequence the sex-biased transcriptome of liver, gills and brain, we provide the first characterization of sex-specific transcriptomes from ~80 stickleback (40 males and 40 females) collected from a natural population during the reproductive period. We find that the liver is extremely differentiated (36% of autosomal genes) and reflects ongoing reproduction, while the brain shows very low levels of differentiation (0.78%) with no particular functional enrichment. Finally, the gills exhibit high levels of differentiation (5%), suggesting that sex should be considered in physiological and ecotoxicological studies of gill responses in fishes. We also find that sex-biased gene expression in X-linked genes is mainly driven by a lack of dosage compensation. However, sex-biased expression of genes that have conserved copies on both sex chromosomes is likely driven by the degeneration of Y allele expression and a down-regulation of male-beneficial mutations on the X chromosome.
2024-06-09 | GSE269432 | GEO
Project description:<p>Papaya is a fruit crop possessing XY sex chromosomes. The development of long </p><p>male peduncles (Mp) is pivotal for the evolutionary transition from gynodioecy to </p><p>dioecy. The gene, CpMp, which controls peduncle length, is one of the four genes </p><p>contributing to the evolution of stage 3 sex chromosomes in papaya. We identified a </p><p>Y-specific SVP paralog, CpSVP-Yp, as a candidate gene for CpMp through </p><p>comparative genomic analyses and functional validation by complementation tests. </p><p>CpMp promotes peduncle elongation by directly activating CpYUC6, an auxin </p><p>biosynthesis gene, thereby increasing IAA levels. Elevated IAA in turn enhance GA, </p><p>triggering expression of the GA stimulated gene CpGASA6, which drives cell division </p><p>and elongation. Overexpression CpGASA6 confirmed its role in peduncle growth but </p><p>revealed a feedback inhibition on IAA biosynthesis. Two upstream regulators of </p><p>CpMp were identified, CpTRAB1, a positive regulator repressed by GA, and </p><p>CpGATA8, a negative regulator upregulated by CpMp, forming two feedback loops. </p><p>Notably, male trees produce 400 times more pollen than hermaphrodites, offering a </p><p>clear fitness advantage. In papaya, three genes - two sex determination genes and this </p><p>long male peduncle gene, are essential for the establishment of dioecy and the </p><p>initiation of sex chromosome evolution. These findings fill a major gap in </p><p>understanding papaya sex chromosome evolution and offer valuable genetic resources </p><p>for papaya improvement. </p>
2025-10-20 | MTBLS13183 | MetaboLights
Project description:The Anopheles mosquito is one of thousands of species in which sex differences play a central role in their biology, as only females need a blood meal in order to produce eggs. Sex differentiation is regulated by sex chromosomes, but their presence creates a dosage imbalance between males (XY) and females (XX). Dosage compensation (DC) can re-equilibrate the expression of sex-chromosomal genes, but because the molecular mechanisms providing DC have only been studied in a few model organisms, key questions about its evolutionary diversity and functional necessity remain unresolved. Here, we reveal the DC pathway in the malaria mosquito Anopheles gambiae. We identified SOA, a previously uncharacterized gene, whose expression is sufficient to induce a global upregulation of X-linked genes. Sex-specific alternative splicing prevents the production of a functional SOA protein in females. The male SOA isoform encodes a DNA-binding protein that recognizes the promoters of X chromosomal genes through a CA repeat sequence. Male mosquitos lacking SOA exhibit a chromosome-wide downregulation of the X, which is compatible with viability, but causes a developmental delay. Thus, our molecular analysis of the first DC master regulator in a non-model organism elucidates the evolutionary steps leading to the establishment of a chromosome-specific fine-tuning mechanism.
2023-07-13 | PXD042353 | Pride
Project description:Background Sex chromosomes are subject to evolutionary pressures distinct from the remainder of the genome, shaping their structure and sequence content. We are interested in the sex chromosomes of domestic pigs (Sus scrofa), how their structure and gene content compares and contrasts with other mammalian species, and the role of gonosomal genes in fertility. This requires an understanding of the XY-homologous sequence on these chromosomes. To this end, we performed microarray-based comparative genomic hybridisation (array-CGH) with male and female Duroc genomic DNA on a pig X-chromosome BAC tiling-path microarray. Putative XY-homologous BACs from regions of interest were subsequently FISH mapped. Results We show that the porcine PAR is approximately 6.5-6.9Mb at the beginning of the short arm of the X, with gene content reflective of the artiodactyl common ancestor. Our array-CGH data also shows an XY-homologous region close to the end of the X long arm, spanning three X BACs. These BACs were FISH mapped, and paint the entire long arm of SSCY. Further clones of interest revealed X-autosomal homology or regions containing repetitive content. Conclusions This study has identified regions of XY homology in the pig genome, and defined the boundary of the PAR on the X chromosome. This adds to our understanding of the evolution of the sex chromosomes in different mammalian lineages, and will prove valuable for future comparative genomic work in suids and for the construction and annotation of the genome sequence for the sex chromosomes. Our finding that the SSCYq repetitive content has corresponding sequence on the X chromosome gives further insight into structure of SSCY, and suggests further functionally important sequences remain to be discovered on the X and Y.
2012-08-30 | GSE40244 | GEO
Project description:We set out to investigate the genetic adaptions of the known marine fungus Paradendryphiella salina CBS112865 to the degradation of brown macro-algae, expecting to find a repertoire of carbohydrate active enzymes highly specialized to the degradation of algal polysaccharides. We performed whole genome, transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina growing on three species of brown algae and under carbon starvation. The genome comparison to close terrestrial fungal relatives, revealed P. salina to have a similar, but reduced carbohydrate active enzyme (CAZyme) profile, except for the presence of three putative alginate lyase 7 genes, most likely acquired via ancient horizontal gene transfer event from a marine bacterium and a polysaccharide lyase 8 gene with similarity to ascomycete chondroitin AC lyases. The proteomic analysis revealed both PL7 and PL8 enzymes to be highly abundant in the algal fermentations together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the base CAZyme repertoire of saprobic and plant pathogenic ascomycetes with the necessary addition of alginate lyases provide the fungi with the enzymatic capabilities to thrive on brown algae polysaccharides and even cope with the algal defense mechanisms.
2019-11-13 | PXD012152 | Pride