Fig. 2

CHH DNA methylation in hybrid and parents. a DNA methylation along chromosomes, calculated from non-overlapping 50 kb bins. Gray columns indicate masked regions represented as Ns in the reference genome. b, c Comparison of CHH methylation for the first 10 Mb of A. thaliana chromosome 1 (b) and A. lyrata chromosome 1 (c). For each panel, the plot on the left is calculated from 5-kb bins, which were divided into two groups based on an arbitrarily set cutoff (blue dash line). Groups 1 and 2 were defined as low and high CHH methylation. The box plots on the right indicate the fractions of annotated transposable elements (TE) (from [49]) in group 1 and 2 bins. d Comparison of CHH DNA methylation between A. thaliana and the hybrid over genes that are downregulated (upper panel) or upregulated (lower panel) in the hybrid. In each plot, genes are scaled so that their transcriptional start sites (TSSs) and transcriptional termination sites (TTSs) are aligned. The y-axis indicates average methylation, calculated from non-overlapping 100-bp windows