Fig. 3: DMP counts and genomic distribution in msh1 memory line.

a Total hyper- and hypomethylation DMP counts in CG, CHG, CHH context embedded in genic regions (gene coding plus 1 kb upstream to start codon, 1 kb downstream to stop codon), TE-related regions (including TEs, TE genes, TE fragments and pseudogenes) and others (including tRNAs, rRNAs, snRNAs, miRNAs, ncRNAs). DMPs were defined as hyper if the site methylation difference in comparisons of each individual to the average of reference plants (the centroid of the wild type group) is greater than 0 and defined as hypo if less than 0. b The relative frequency of DMPs in genic regions (blue shades), TE-related regions (in red shades) and others (in green shades). The average of five wild-type plants (the centroid of the wild-type group) was used as a reference for each generation. The relative frequency of DMPs in each genomic feature was estimated as the number of DMPs divided by the number of total genomic cytosine positions in each genomic feature. Each individual’s DMP number and frequency is computed separately and the group mean for WT (wild type) and MM (msh1 memory) are presented. Notice that DMPs are detected within wild-type samples due to spontaneous variation, distinct from treatment-induced, is detectable within our system. Source data underlying Fig. 3a, b are provided as a Source Data file.