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Plant Y-chromosome degeneration is retarded by haploid purifying selection.

ABSTRACT: 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.

ORGANISM(S): Silene vulgaris Silene latifolia

PROVIDER: GSE30958 | GEO | 2012/07/30

SECONDARY ACCESSION(S): PRJNA146235

REPOSITORIES: GEO

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Plant Y-chromosome degeneration is retarded by haploid purifying selection.

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

Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes

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

Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes

2012-08-24 | GSE35563 | GEO

Plant Y-chromosome degeneration is retarded by haploid purifying selection.

Project description:Plant Y-chromosome degeneration is retarded by haploid purifying selection.

| PRJNA146235 | ENA

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

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:Identification of sex-determining factor in Marchantia revealed unique evolution of the genes linked to sex chromosomes in a haploid system

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Project description:Identification of sex-determining factor in Marchantia revealed unique evolution of the genes linked to sex chromosomes in a haploid system

| PRJNA757569 | ENA

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells.

2011-10-06 | GSE32663 | GEO

Sex-biased gene expression in 18 day embryonic chicken heart, brain, and gonad

Project description:The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes. In many organisms dosage compensation has thus evolved to equalize sex-linked gene expression in males and females1,2, in mammals achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. Another form of dosage compensation ensures that expression levels on the X chromosome and on autosomes are balanced3,4. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma5,6. Here we use a microarray approach to show that male day 18 chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4-1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci2. Intriguingly, without global dosage compensation, female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds. The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination. Keywords: dosage compensation, sex-biased gene expression, soma and gonad

2007-08-07 | GSE8693 | GEO

Sex-specific embryonic gene expression in species with newly evolved sex chromosomes

Project description:Sex-specific embryonic gene expression in species with newly evolved sex chromosomes

| PRJNA232085 | ENA