DNA isolation and sequencing

We extracted DNA from the gonads of 3-month-old C. picta hatchlings (ten males and ten females, and pooled in groups of five hatchlings for replication) using the Gentra Puregene DNA extraction kit (Gentra) following the manufacturer’s instructions. DNA was processed by BGI Americas following the MeDIP protocol [104] where DNA was fragmented and denatured, and the methylated DNA was immunoprecipitated using the MagMEDI kit (Diagenode). A positive control (methylated DNA) and a negative control (unmethylated DNA) were used at the MeDIP step to ensure that the MeDIP worked properly. The methylated DNA was size selected (100–300 bp) and sequenced using the Illumina HiSeq paired-end protocol. We obtained between 126 million and 163 million 50-bp reads per library amounting to a total of ~564 million reads (Table 1).