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).