Fig. 3: Differentially methylated position genomic distribution and enriched differentially methylated gene networks in graft progenies.

a The relative frequency of differentially methylated positions (DMPs) in each graft progeny plant over genic regions (blue shades), TE-related regions (red shades), and others (green shades). The average of three control plants (the centroid of Col-0/Col-0 graft progenies) was used as reference. The relative frequency of DMPs in each genomic feature were estimated as the number of DMPs divided by the number of total genomic cytosine positions in each genomic feature. DMP number and frequency of each individual was computed separately and the group means for Col-0/Col-0 graft progenies and Col-0/msh1 graft progenies are presented. Upper part of the graph shows the distribution of hyper DMPs, the lower part shows the distribution of hypo DMPs. b The relative frequency of DMPs in each graft progeny plant over genic regions (blue shades), LTR retrotransposon regions (red shades), and others (green shades). The average of three control plants (the centroid of Rutgers/Rutgers graft progenies) was used as reference. The tomato LTR retrotransposon annotation was acquired by using LTRpred version 1.1.0.⁶⁹ Networks identified by Network Enrichment Analysis Test (NEAT) for the DMGs identified in c Arabidopsis graft progeny (Col-0/msh1 vs. Col-0/Col-0); d tomato graft progeny (R/msh1 vs. R/R); e three networks shared by both Arabidopsis and tomato graft progenies. Bar graph represents number of differentially methylated genes (DMGs) and dotted line represents −log₁₀(p-value) of the enrichment test. c–e p-values were computed using one-sided hypergeometric distribution test as implemented in NEAT (R package version 1.1.3). Source data are provided as a Source Data file.