Indication of family-specific DNA methylation patterns in developing oysters

Background DNA methylation is an epigenetic modification that is ubiquitous across many eukaryotes, with variable patterns and functions across taxa. The roles of DNA methylation during invertebrate development remain enigmatic, especially regarding the inheritance and ontogenetic dynamics of methylation. In order to better understand to what degree DNA methylation patterns are heritable, variable between individuals, and changing during Crassostrea gigas development, we characterized the genome-wide methylome of Crassostrea gigas sperm and larvae from two full-sib families nested within a maternal half-sib family across developmental stages. Results Bisulfite treated DNA sequencing of Crassostrea gigas sperm and larvae at 72 hours post fertilization and 120 hours post fertilization revealed DNA methylation ranges from 15-18%. Our data suggest that DNA methylation patterns are inherited, as methylation patterns were more similar between the two sires and their offspring compared to methylations pattern differences among developmental stages. Loci differing between the two paternal full-sib families (189) were found throughout the genome but were concentrated in transposable elements. The proportion of differentially methylated loci among developmental stages was not significantly greater in any genomic region. Conclusions This study provides the first single-base pair resolution DNA methylomes for both oyster sperm and larval samples from multiple crosses. Assuming DNA methylation is introduced randomly, the predominance of differentially methylated loci between families within transposable elements could be associated with selection against altering methylation in gene bodies. For instance, differentially methylated loci in gene bodies could be lethal or deleterious, as they would alter gene expression. Another possibility is that differentially methylated loci may provide advantageous phenotypic variation by increasing transposable element mobility. Future research should focus on the relationship between epigenetic and genetic variation, and explore the possible relationship of DNA methylation and transposable element activity.