Fig. 1

Gene body methylation at individual CGs in Col and Cvi. a Smoothed scatterplot of average CG methylation in Col versus Cvi for individual CGs within gene bodies (top) or transposable elements (TEs; bottom). CGs in the four corners of the top plot are used in b. Number of cytosines in each corner: Col−, Cvi − = 673,701; Col−, Cvi + = 10,500; Col+, Cvi − = 79,667; Col+, Cvi + = 51,575. Total CGs in genic plot = 867,234. b Hierarchical clustering of the 22,149 genes with at least ten CGs classified into any of the four categories in a. Rows represent genes, columns represent the four categories in a, and color represents fraction of CGs in each of the four categories for each gene. Genes were grouped into seven clusters. c Average non-CG methylation levels among genes in different clusters from b