Fig. 3: The DNA methylation landscape of Welwitschia and dynamic reprogramming between tissues mediated by the RNA-directed DNA methylation machinery.

a The level of CG methylation varies >75%, whilst CHG and CHH methylation varies >25%, over at least five informative sequenced cytosines. Heat maps showing CG, CHG, and CHH methylation in the basal meristem of a male individual sampled in the wild (MM1), a young leaf from a male individual (the newly emergent region, MY1), and a male individual from the greenhouse, including the central region of the basal meristem (CM), the peripheral part of the basal meristem (PM) and leaf (L). Methylation levels were calculated and presented in 1 Mb windows, with the maximum set to be the highest value among the  five tissues in each 1 Mb window (maximum values were: 4,619 (methylated CG); 7,552 (methylated CHG), 56,186 (methylated CHH)). b Box plots showing the variation of CG, CHG, and CHH methylation among different tissues (each box shows the median methylation value (horizontal line) ± SD) and whiskers on vertical lines show minimum and maximum values). Data were analyzed from the total number of CG, CHG, CHH methylation sites from n = 7 biologically independent samples (MM1, FM1 (basal meristem of a female individual), MY1, FY1 (young leaf of a female individual), CM, PM, L). c Differentially methylated region (DMR) statistics of methylated cytosines at CHH trinucleotides in the genome. (left) The proportion of methylated cytosines that are differentially methylated between individuals in different genomic domains, and (right) the proportion of DMR at CHH trinucleotides occurring in transposable elements (TEs). d Most genes involved in canonical and non-canonical methylation mediated by the RdDM pathway (y axis) show increased transcript abundance (upregulated red, downregulated blue) in meristematic tissues compared with young leaves.