Fig. 2

a RPKM heatmap of differentially methylated genes in Chrysemys picta (rows) clustered by mean methylation level per gene. Methylation levels were scaled to [−1.5, 1.5] to indicate genes undergoing high (green) and low (red) relative methylation. b Normalized CpG content of all annotated genes (red), experimentally verified to be methylated using MeDIP-seq (yellow) and differentially methylated (purple). c Fold change in methylation (red: hypermethylated in female; green hypermethylated in male) as seen in gene bodies (exons + introns), exons only, introns only and promoters. d Examples of genes possessing multiple windows that displayed sex-specific methylation. e, f Scatterplot of normalized CpG content (nCpG) in methylated windows occurring (e) in gene bodies relative to nCpG of gene bodies and f in promoters relative to nCpG of the complete promoter sequence (~5 kb upstream). Differentially methylated windows in hatchlings are overlaid, with those hypermethylated in males indicated in blue, and those hypermethylated in females indicated in red