(A) Bar chart depicting total abundance (top) and heat map of individual relative transcript levels (bottom) of genes involved in CG methylation in three biological replicates each of flowers, embryos, and leaves (Hofmann et al., 2019). fb, floral buds; pg, preglobular; gl, globular; eh, early heart; lh, late heart; et, early torpedo; lt, late torpedo; bc, bent cotyledon; mg, mature green; lf, leaf. (B) Heatmap showing developmental dynamics of permuted gene set (top) median values (i.e. 1000 iterations of random sampling of 25 genes) and top-25 genes co-varying with MET1, VIM1, VIM2, and VIM3 obtained by employing nearest neighbor algorithm calculated based on Euclidean distance between genes and centroid expression of MET1, VIM1, VIM2, and VIM3 (bottom). (C) Sequence logo representing nucleotide probability relative to differentially methylated cytosines (DMC). (D) Proportion of CG and CHG differentially methylated regions (DMRs) overlapping genomic features. Venn diagram showing overlap between CG and CHG DMRs. Significance overlap of DMRs determined by Fisher's Exact test p value < 0.0001 is indicated by ****. (E and F) Violin plot showing CG (top) and CHG (bottom) methylation differences between mutant and WT leaves for CHG DMRs overlapping (E) or not overlapping (F) with CG DMRs (Stroud et al., 2013). (G and H) Box plots of average weighted methylation of CG DMRs (n = 1185) and (G) CHG DMRs (n = 1398) during development. fb, floral buds; pg, preglobular; eh, early heart; tp, torpedo (6 DAP) Pignatta et al., 2015; bc, bent cotyledon; lt-mg, late torpedo-to-early mature green Hsieh et al., 2009; mg, mature green Bouyer et al., 2017; lf, leaf. fb, pg, eh, bc and lf were from Bouyer et al., 2017; Hsieh et al., 2009; Papareddy et al., 2020; Pignatta et al., 2015. Unless stated as not significant (ns), all combinations are significant with p values < 0.001 obtained by Mann-Whitney U test. Shaded horizontal line in the background represents the median methylation value of floral buds.