Plant Y-chromosome degeneration is retarded by haploid purifying selection.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA146235 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR316280.fastq.gz | Fastqsanger.gz | |||
| SRR316281_1.fastq.gz | Fastqsanger.gz | |||
| SRR316281_2.fastq.gz | Fastqsanger.gz | |||
| SRR316282.fastq.gz | Fastqsanger.gz | |||
| SRR316283_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Sex chromosomes are subject to unique evolutionary forces that cause suppression of recombination, leading to sequence degeneration and the formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although progress has been made in characterizing the outcomes of these evolutionary processes on vertebrate sex chromosomes, it is still unclear how recombination suppression and sequence divergence typically occur and how gene dosage imbalances are resolved in the heterogametic sex. The threespine stickleback fish (Gasterosteus aculeatus) is a powerful model system to explore vertebrate sex chromosome evolution, as it possesses an XY sex chromosome pair at relatively early stages of differentiation. Using a combination of whole-genome and transcriptome sequencing, we characterized sequence evolution and gene expression across the sex chromosomes. We uncovered two distinct evolutionary strata that correspond with known structural rearrangements on the Y chromosome. In the oldest stratum, only a handful of genes remain, and these genes are under strong purifying selection. By comparing sex-linked gene expression with expression of autosomal orthologs in an outgroup, we show that dosage compensation has not evolved in threespine sticklebacks through upregulation of the X chromosome in males. Instead, in the oldest stratum, the genes that still possess a Y chromosome allele are enriched for genes predicted to be dosage sensitive in mammals and yeast. Our results suggest that dosage imbalances may have been avoided at haploinsufficient genes by retaining function of the Y chromosome allele through strong purifying selection.
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