PAG 2022: Polyploidy and environmental stress have distinct impacts on Pacific oyster ctenidia methylomes

Presentation given at PAG 2021 Aquaculture Workshop Production of polyploid organisms resilient to environmental change requires a molecular understanding of stress response mechanisms. This is especially important when considering the use of triploid oysters in commercial aquaculture settings. Examination of DNA methylation can elucidate gene expression regulation mechanisms employed by triploid oysters, and how they may differ from their diploid counterparts. We examined how artificial genome duplication and environmental variation contribute to stress response phenotypes in the Pacific oyster (Crassostrea gigas). We exposed diploid (n = 12) and triploid (n = 12) C. gigas to low or high pH stress for six weeks. Ctenidia methylomes were then obtained using whole genome bisulfite sequencing. Distinct differentially methylated loci (DML) were associated with ploidy status (154 ploidy-DML) and pH condition (178 pH-DML). Functions of genes containing ploidy-DML were not similar to those observed in organisms that undergo natural polyploidization. Genes with pH-DML were associated with apoptosis, protein ubiquitination, zinc ion binding, and cytoskeletal processes commonly observed in oyster response to ocean acidification. Given the enrichment of both ploidy- and pH-DML in genes with multiple transcripts, it is possible that these methylation changes can influence gene expression and physiological phenotype. Our study — which is the first to provide single base-pair resolution assessment of diploid and triploid methylomes in a marine invertebrate and provides information useful for improving triploid production — suggests that while methylation may play different regulatory roles during artificial and natural genome duplication events, environmentally-sensitive methylome responses may be uniform between diploid and triploid C. gigas.