Fig. 6

Correlation between structural variants (SVs) and DNA methylation. a Structural variants (SVs) were analyzed for Col SR. The proportion of each SV was indicated as %. Unclassified are the regions not included in other SVs. “Col” indicates the composition of Col ref. genome. b DNA methylation dynamics of each SV during seed ripening and germination were analyzed. The average level of methylation is represented as dots and linked with a line (b, d). c Average 24-nt small RNA expression level of Col samples overlaps with CR or Col SR. “Col SR (CG|CHG|CHH)” indicates genomic loci covered by at least one of three types of cytosine methylation context windows in Col SR, and these loci were used to find 24sRCs overlap with Col SR. 24sRCs that did not overlap with “Col SR (CG|CHG|CHH)” loci were treated as CR-overlapping 24sRCs. d CHH methylation differences between wild type and RdDM machinery mutants in SV-overlapping CR and Col SR. Sequence-gain type SVs in Col SR were more hypomethylated than those in CR in mutants