DNA methylation frequency and epigenetic variability of the Pacific oyster Crassostrea gigas in relation to the gametogenesis

The origin and maintenance of sexual gametogenesis might provide insights into eukaryote evolution. Epigenetic variation of eukaryote well-being would provide clues that could relate ecological and evolutionary processes. To investigate the relationship between gametogenic variability and epigenetic polymorphism in the Pacific oyster Crassostrea gigas, DNA methylation differences were represented by analyzing genome-wide methylation patterns using the fluorescent-labeled methylation sensitive-amplified polymorphism (F-MSAP) technique. The C. gigas genome was widely methylated and marked variations in the pattern of methylation were shown during female and male gonad development. Statistically, the total methylation level increased from early developing stage to resorbing stage, from 28.86 to 34.53% in ovaries, while it increased from 31.20 to 35.46% in this period in testes. The unweighted pair group method with arithmetic mean and principal coordinate analysis separated the C. gigas during female and male gonad development remarkably well, indicating remarkable differences across gametogenesis between ovaries and testes. Variation was higher in testes than in ovaries by the frequency based and multivariate analyses above. Both multivariate analyses and a significantly different population epigenetic structure suggested that a striking difference might exist across gametogenesis, reflecting a turning point of the methylation mechanism during reproductive progress. This study provides some information on the role of DNA methylation in the potential mechanism during female and male gonad development.