Ontology highlight
ABSTRACT:
PROVIDER: PRJNA804573 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17951400.fastq.gz | Fastqsanger.gz | |||
| SRR17951401.fastq.gz | Fastqsanger.gz | |||
| SRR17951402.fastq.gz | Fastqsanger.gz | |||
| SRR17951403.fastq.gz | Fastqsanger.gz | |||
| SRR17951404.fastq.gz | Fastqsanger.gz |
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Project description:Sex determination is the process by which and original bipotential gonad differentiate into either a testis or ovaries. While mammals and birds determine their sex solely by genetic clues (genetic sex determination, GSD), other vertebrates like the turtle Trachemys scripta are influenced by environmental factors, like temperature (environmental sex determination, ESD). In both cases an initially bipotential gonad develops into either testes or ovaries in response to GSD or ESD cues. In order to shed light into the differences and similarities between sex determination systems we performed single-cell RNA-seq on Trachemys scripta developing gonads during the sex determination window.
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Project description:Sex dimorphism is a diversification that can be observed in single species of gonochoristic animals. Phylum Tardigrada exhibits remarkable diversity in sex dimorphism in its morphology and behavior. Despite the wealth of genomic and zoological knowledge accumulating, sexual genetic differences of tardigrades have been identified yet. In this study, we focused on the gonochoristic species Paramacrobiotus metropolitanus, employing omics analyses to unravel the basis of sex differences. Approximately 2,000 male-biased expression genes were concentrated in 29 non-male-specific genomic loci, of which two paralogs of a new Doublesex-Mab-3-related (DM) subfamily specific to Macrobiotidae were discovered. We also identified several tardigrade specific anhydrobiosis genes exhibiting sex-biased　expression, suggesting a potential role in protecting sex-specific gametes. The existence of male-biased, but not male specific genomic loci and the limited conservation of the newly identified dimorphically-expressed DM subfamily would provide the foundation for understanding the diverse sex determination cascade in tardigrades.
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Project description:Purpose: Determine whether sex-determining genes are bivalent at the bipotential stage, poised between the testis and ovary fate, and whether H3K4me3 and H3K27me3 resolve into sex-specific patterns after sex determination, contributing to the canalization and stabilization of either the testis or ovary fate. Methods: XX and XY supporting cells of the gonad were FACS-purified before sex determination (at E10.5) and after sex determination (at E13.5), and submitted to ChIP-seq for H3K4me3, H3K27me3 and H3 as a means to normalize across cell populations. Results: We found that key sex-determining genes are bivalent at the bipotential stage. Genes that are upregulated affter sex determination are stripped of their repressive H3K27me3 mark, whereas repressed genes that promote the alternate pathway remain bivalent even after sex determination.
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Project description:The extraordinary range in the degree of sexual dimorphism (SD) among animal species is widely perceived to be caused in part by differences in patterns of sexual selection, but sex-specific adaptations and sex chromosome differences also play a role. Studies in insects have discovered a substantial number of sex-biased genes, but little is known about the epigenetic basis of SD. The degree and genome-wide distribution of sex-biased expression become interesting questions in hymenoptera species with haplodiploid sex-determination. To study the genetic and epigenetic architecture of SD and understand the conservation and evolution of sex-biased expression in a haplodiploid system that lacks sex chromosomes, we performed RNA-seq and whole-genome bisulfite sequencing in female and male adult samples of two parasitoid wasp species, Nasonia vitripennis and Nasonia giraulti. More than 75% of the expressed genes displayed significantly sex-biased expression. Both the number and the degree of sex-biased genes are higher than insects like Drosophila melanogaster, which have sex-chromosome mediated sex determination. Females from the two Nasonia species have far more similar expression profiles than does the contrast between the two sexes within either species. Interestingly, the extremely male- and female-biased genes are enriched for totally different functional categories: male-biased genes are highly enriched for key enzymes in sex-pheromone synthesis; female-biased genes are enriched for nuclear-located genes that are responsible for epigenetic regulation of gene expression. Unlike gene expression profiles, DNA methylomes are more similar within species, and no stable differentially methylated genes have been found between the two sexes, suggesting that DNA methylation is not directly responsible for the molecular basis of SD. However, methylation status does influence sex-biased expression: 80% of female-biased genes are methylated, which is more than two-fold higher than the genome average (30%); almost all male-biased and sex-specific genes are non-methylated, which is consistent with the fact that methylated genes have house-keeping functions and a broader expression breadth. Evolutionarily, male-biased genes have greater sequence divergence between the two species, and they are more likely to have a functional paralog in the Nasonia genome. Sex-specific genes have significantly higher non-synonymous substitution rates and dN/dS ratios. In addition, local clusters of sex-biased genes in the genome may have epigenetic properties similar to the sex chromosome. In summary, Nasonia accomplish a striking degree of sex-differential expression through a difference in ploidy along with associated differences in methylations status. Whole-genome bisulfite sequencing of 24-hour adult whole body samples of Nasonia vitripennis and Nasonia giraulti using Iilumina sequencing.
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