Genomic distribution of mCGs. (A) Density of mCG across scaffold172 in the inbred sample. A 1-kb non-overlapping sliding window was used for density estimation, which was calculated as the number of identified mCGs divided by the total length of a window. (B) Methylation levels of different genomic elements. The 'gene body’ category includes untranslated regions (5’-UTR and 3’-UTR, i.e. non-coding exonic regions), coding sequences (CDS, i.e. coding exonic regions) and introns, and the 'other’ category represents all genomic regions excluding gene bodies, 2-kb up/downstream of gene bodies, repeats, tRNAs, snRNAs and rRNAs. (C) Methylation levels of different repeat classes. 'Background’ corresponds to the 'other’ category in panel B. (D) Methylation levels of repeat loci with different divergence rates. The repeat divergence rate was calculated between the identified repetitive elements in the oyster genome and the consensus sequences in the repeat library .