Genome-wide DNA methylation profiling reveals epigenetic regulation of sex differentiation and gonadal development in Apostichopus japonicus

The sea cucumber (Apostichopus japonicus) is an economically important marine benthic echinoderm. Understanding the molecular mechanisms of sex determination and differentiation is critical for improving sex-controlled breeding strategies. Epigenetic modifications serve as a crucial link between an organism's genetic information and environmental cues, playing a fundamental role in determining sex fate and conferring sexual plasticity across various species. The echinoderms exhibit an extremely diverse reproductive strategies, including both sexual reproduction and asexual reproduction. However, the molecular mechanisms governing epigenetic regulation in the sex differentiation process within echinoderms remain elusive. Here, we integrated genome-wide DNA methylation profiling and transcriptomic analysis of mature male and female gonads to investigate epigenetic regulation during sex differentiation. We identified 12,605 differentially methylated regions (DMRs) and 2764 differentially methylated genes (DMGs). By comparing the methylation levels of genes with different expression patterns, non-specific, or housekeeping genes, show high methylation in gene body region, while specifically expressed genes have lower methylation, which suggested that CpG methylation targeting housekeeping genes preferentially. Protein-protein interaction networks and functional enrichment analysis of differentially expressed methylated genes (DEMGs) revealed significant associations with sex-related processes, including steroid metabolism (hsd17β4, cyp17a1), meiosis (dmc1, mei4, msh4), spermatogenesis (cfap, kif families), and oogenesis (fmn2, igf2bp3). Our findings demonstrate that DNA methylation dynamically regulates transcriptional programs governing sex differentiation in A. japonicus, providing a molecular basis for enhancing reproductive management in sea cucumber aquaculture.