Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Oryza sativa ssp. indica Illumina lwhole-genome bisulfite sequencing used for coverage comparison next to the method plant-RRBS

ABSTRACT: The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for comparative coverage aspects with plant-RRBS methylome profiling by bioinformatics analyses. The inbred control line and a derived epiline LR2 of the 4th selfing were analysed using whole-genome bisulfite sequencing.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Oryza sativa Indica Group

SUBMITTER: Mieke Van Lijsebettens

PROVIDER: E-MTAB-5002 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.

Schmidt Martin M Van Bel Michiel M Woloszynska Magdalena M Slabbinck Bram B Martens Cindy C De Block Marc M Coppens Frederik F Van Lijsebettens Mieke M

BMC plant biology 20170706 1

<h4>Background</h4>Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hyd ...[more]

PMID: 28683715

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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.

Dataset Information

Oryza sativa ssp. indica Illumina lwhole-genome bisulfite sequencing used for coverage comparison next to the method plant-RRBS

Publications

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.

Similar Datasets

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