Fig. 2

Dynamic epigenetic reconfiguration during seed development and germination. a–c Methylation levels within sdev DMRs. d, e Methylation levels germin DMRs. a mCG within CG DMR, b, d mCHG within CHG DMR, c, e mCHH within CHH DMR. Number of DMRs and total length of DMRs are indicated. Wilcoxon rank sum tests were applied to subsequent stages. Only non-significant pairs were indicated by “ns,” otherwise the methylation levels were significantly different (p < 0.05) between stages. f The fraction of genomic features overlapping with DMRs. g, h Venn diagrams showing overlap between sdev DMRs and germin DMRs. g CHG DMR and (h) CHH DMR. Overlap between sdev DMRs and germin DMRs were significant (permutation test with 1000 trials: p < 0.001 and p < 0.001, respectively). i A representative TE showing the gain of CHH methylation during seed development (top) and the loss of CHH methylation during germination (bottom). j, k Heatmaps showing CHH methylation levels within sdev DMRs and germin DMRs, respectively. DMRs were sorted by average methylation levels