Differential methylation between parental environments
After quality filtering, approximately 378 million reads were retained (range: 6-25 million), averaging 12.5 million reads per sample. Of those, approximately 61.1% were uniquely mapped reads to the reference genome. Overall bisulfite conversion efficiency was 99.5% (Table S1). In total, we identified 5.5 million cytosine sites of which 39,205 CpG sites matched the coverage requirements. The majority of the cytosines surveyed mapped gene bodies (71.12%) or intergenic regions (12.61%), while 2.61% were located on putative promoters.
Parental methylation profiles significantly differed in 1,854 methylated cytosines (DMCs) between environments. Unsupervised hierarchical clustering of these DMCs revealed clear distinctive methylation profiles between environments (Fig. S3). Most of these DMCs were overlapping gene bodies (69.69%), followed by intergenic regions (7.19%) and putative promoters (2.56%). The number of DMCs identified in 4,000 randomly generated parental groups was in all cases lower than 1,854 with an average of 247.3 (s.d. ±158.5), indicating that the DMCs identified between environments was significantly higher than expected by chance (P<0.001).