Ontology highlight
ABSTRACT:
PROVIDER: PRJNA757569 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15603443.fastq.gz | Fastqsanger.gz | |||
| SRR15603444.fastq.gz | Fastqsanger.gz | |||
| SRR15603445.fastq.gz | Fastqsanger.gz | |||
| SRR15603446.fastq.gz | Fastqsanger.gz | |||
| SRR15603447.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Sex chromosomes evolved many times independently in many different organisms. According to the currently accepted model, X- and Y-chromosomes evolve from a pair of autosomes via a series of inversions leading to step-wise expansion of a non-recombining region on the Y chromosome (NRY) and the consequential degeneration of genes trapped in the NRY. Our results suggest that plants represent an exception to this rule due to their unique life-cycle that includes alteration of diploid and haploid generations and widespread haploid expression of genes in plant gametophytes. Using a new high-throughput approach we identified over 400 new genes expressed from X- and Y- chromosomes in Silene latifolia, a plant that evolved sex chromosomes about 10 million years ago. Y-linked genes show faster accumulation of amino-acid replacements and loss of expression, compared to X-linked genes. These degenerative processes are significantly less pronounced in more constrained genes and genes that are likely exposed to haploid-phase selection. This may explain why plants retain hundreds of expressed Y-linked genes despite millions of years of Y-chromosome degeneration, while animal Y-chromosomes are almost completely degenerate.
2012-07-30 | GSE30958 | GEO
Project description:Sex chromosomes evolved many times independently in many different organisms. According to the currently accepted model, X- and Y-chromosomes evolve from a pair of autosomes via a series of inversions leading to step-wise expansion of a non-recombining region on the Y chromosome (NRY) and the consequential degeneration of genes trapped in the NRY. Our results suggest that plants represent an exception to this rule due to their unique life-cycle that includes alteration of diploid and haploid generations and widespread haploid expression of genes in plant gametophytes. Using a new high-throughput approach we identified over 400 new genes expressed from X- and Y- chromosomes in Silene latifolia, a plant that evolved sex chromosomes about 10 million years ago. Y-linked genes show faster accumulation of amino-acid replacements and loss of expression, compared to X-linked genes. These degenerative processes are significantly less pronounced in more constrained genes and genes that are likely exposed to haploid-phase selection. This may explain why plants retain hundreds of expressed Y-linked genes despite millions of years of Y-chromosome degeneration, while animal Y-chromosomes are almost completely degenerate. We used a combination of Illumina sequencing of cDNA (RNAseq) and segregation analysis of SNPs identified from RNAseq to identify sex-linked genes in plant Silene latifolia. The experiment involved RNAseq from male and female parents and F1 progeny for two genetic crosses. We submit raw data in fastq format for 11 samples. Four of these samples are single end Solexa reads (a single file per sample) and seven samples were sequenced with paired end Solexa sequencing (two fastq files per sample) - 18 files in total.
2012-07-30 | E-GEOD-30958 | biostudies-arrayexpress
Project description:Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution. Additionally, we test for the presence of Y-specific small RNA loci in several XX, XY, and YY genotypes that may be acting as sex determination loci.
2020-05-02 | GSE149730 | GEO
Project description:Birds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. Here we report functional in vivo and evolutionary analyses of a Z-chromosome-linked microRNA (miR-2954) with strongly male-biased expression that was previously proposed to play a key role in sex chromosome dosage compensation1. We knocked out miR-2954 in chicken, which resulted in early embryonic lethality of homozygous knockout males, likely due to the highly specific upregulation of dosage-sensitive Z-linked target genes of miR-2954. Our evolutionary gene expression analyses further revealed that these dosage-sensitive target genes have become upregulated on the single Z in female birds during evolution. Altogether, our work unveils a scenario where evolutionary pressures on females following W gene loss led to the evolution of transcriptional upregulation of dosage-sensitive genes on the Z not only in female but also in male birds. The resulting overabundance of transcripts in males resulting from the combined activity of two dosage-sensitive Z gene copies was in turn offset by the emergence of a highly targeted miR-2954-mediated transcript degradation mechanism during avian evolution. Our findings demonstrate that birds have evolved a unique sex chromosome dosage compensation system in which a microRNA has become essential for male survival.
2024-04-17 | GSE257549 | GEO
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene
2012-12-06 | GSE42785 | GEO
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene
2012-12-06 | GSE42779 | GEO
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene
2012-12-06 | GSE42494 | 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.
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