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Background   Daphnia  species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female  Daphnia  can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male  Daphnia pulex  under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders.    Results  In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male  Daphnia  are dominated with epigenetic modifications that globally promote elevated gene expression, while female  Daphnia  are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female  Daphnia . Furthermore, H3K4me3 modifications are higher in male compared to female  Daphnia  in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male  Daphnia  in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes.    Conclusions  The epigenetic differences between male and female in  Daphnia pulex  are vast and dominated by changes that promote elevated gene expression in male  Daphnia . Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex