Differential DNA methylation in Pacific oyster reproductive tissue associated with ocean acidification

Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change are experienced by coastal ecosystems. Environmentally-induced changes to the methylome can regulate gene expression, but methylome responses may be tissue- and species-specific. To assess how ocean acidification affects the Pacific oyster ( Crassostrea gigas ) epigenome, we exposed oysters to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for seven weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C->T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1,284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation. ### Competing Interest Statement The authors have declared no competing interest. * WGBS : whole genome bisulfite sequencing DML : differentially methylated locus/loci SNP : single nucleotide polymorphism