Identifying Differentially Methylated Regions in P. tricornutum

Differentially methylated regions were called using the DMRcaller R package v1.22.0⁴⁵ . Given the low level of correlation of DNA methylation observed in P. tricornutum^{11 (link),27 (link)} and sequencing coverage in all three cell lines, only cytosines with coverage > =5X in all three lines were kept for further analysis and the bins strategy was favored over other built-in DMRcaller tools. DMRs were defined as 100 bp regions with at least an average 20% loss/gain of DNA methylation in either one of the DNMT5:KOs compared to the reference strain. The ‘Score test’ method was used to calculate statistical significance and threshold was set at p < 0.01. In addition, to distinguish isolated differentially methylated cytosines from regions with significant loss of DNA methylation, an hypoDMR must contain at least methylated 2 CpG in the reference strain.