Cumulative effects and geographic distribution of mCHG-decreasing alleles.

(A) Cumulative effect on mCHG|mCHH. Chr1:4035022 (JMJ26) was excluded from the analysis of CMT2-targeted transposons as it has no effect. Chr5:2355910 was used for MSI1. Inserted plots show mCHG levels around transposons, calculated using 20 sliding windows across the transposon body and flanking regions. (B) Longitudinal frequency distribution of mCHG-decreasing and NRPE1’ alleles (top); geographical distribution of the number of mCHG-decreasing alleles (middle), and mCHG|mCHH levels in RdDM-targeted transposons (bottom). Triangles correspond to lines in the inserted plot of panel D. (C) The frequency of distribution of the number of mCHG-decreasing alleles, separately for NRPE1’ genotypes. (D) The number of recent transposon insertions [22] as a function of NRPE1’ genotype and the number of mCHG-decreasing alleles. Significance was tested using a permutation test (see Methods; *** is p p NRPE1’ non-reference allele. Filled circles indicate mCHH- or mCHG-decreasing alleles. Mapping and statistical testing were performed in R version 3.5.3. Maps were generated using the following packages: maps, ggridges, ggplot, rasrer, tidyverse.