Fig. 3

The involvement of DNA methylation in gene transcript during pear flesh development. a DNA methylation levels of genes and TEs in the fruit flesh at 11 stages (from S1 to S11). b Analysis of the differentially expressed genes (DEGs) correlated with DNA methylation in the promoter. The percentage represents the proportion of the DEGs that were correlated or uncorrelated with DNA methylation in the promoter. c Flesh callus was treated by the DNA methylation inhibitor 5-azacytidine (5’-Aza). Control is the untreated callus. d Genome-wide bisulfite sequencing of 5’-Aza-treated and control calli revealed the changes in DNA methylation. Standard error bars were calculated based on three replicates. Analysis of variance were calculated by Student’s t-test. Single asterisk stand for the level of significance at P-value < 0.05. e Chromosome locations of DNA methylation sites and all predicted genes revealed the genes modified by DNA methylation of all three context (CG, CHG, and CHH). Chr 1ꟷ17 represent the 17 chromosomes in pear genome. f A diagram showed the ratio of upregulated and downregulated genes between S1 and later stages. These genes have been identified to be repressed by 5’-Aza treatment in fruit callus and to be modified by DNA methylation in developing fruits. g A venn diagram showed the number of the DEGs modified by CG, CHG, and/or CHH methylations