Fig. 7

DNA methylation in callus and seedling tissues. a–c Distribution of cytosine methylation in three sequence contexts (CG, CHG, and CHH) around genes in two biological replicates of the callus (orange) and two biological replicates of the seedling (green). An average methylation rate per window across all examined genes was determined and plotted versus the window order. A window in the gene body is 1/200 of the gene body. A window outside of the gene body is 20 bp. d–f Violin plots of methylation on repetitive sequences. For each violin plot, the top half is the distribution of methylation in the callus and the bottom half is the distribution of methylation in the seedling. Each dot represents the median of methylation rates. Numbers stand for the mean methylation differences between the callus and the seedling, which are color-coded with blue and red to represent increased methylation and decreased methylation in the callus, respectively. All differences are significant (p-value < 0.0001) by paired t-test. g Barplots of DMRs on genic regions, including 2 kb beyond each of TSS and TTS, and the rest of the genome (intergenic regions). h Distribution of DMR sequences around genes. The definition of the gene body is the same as described in a–c. i Proportions of DE genes up-regulated in hyper DMR and hypo DMR regions (gene body, 1 kb 5′ upstream and 1 kb 3′ downstream regions). Numbers on top of bars are numbers of DE genes. Stars indicate significance (p < 0.05) from χ² tests for the independence of the DMR and DE changing directions. In g, h, and i, hyper and hypo stand for increased and decreased methylation in the callus relative to the seedling, respectively