Abstract
The roles of DNA methylation during invertebrate development remain enigmatic, especially regarding the inheritance and ontogenetic dynamics of methylation. Here, 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 several developmental stages. Our data suggest that DNA methylation patterns are inherited, as methylation patterns were similar between the two sires and their offspring. Loci differing between the two paternal full-sib families (189) and among the developmental stages (160) were found throughout the genome but were concentrated in transposable elements and repeat regions. We suggest that the predominance of differentially methylated loci within transposable elements is a result of selection against changes in gene body methylation.