Fig. 1

The distribution patterns of DNA cytosine methylation levels in the pear genome. a The density distribution of DNA methylation levels in three contexts (CG, CHG, and CHH), gene density, and TE density on the 17 pear chromosomes. b The average rates of methylated cytosines (mC) in the three contexts in the pear genome for the three pear populations (wild, landrace, and improved). c Comparisons of methylation levels of the three contexts in the wild, landrace, and improved populations (*P < 0.05; **P < 0.01; ***P < 0.001, two-tailed paired Student’s t-test). d Distribution of DNA methylation levels across the upstream 2 kb, gene body, and downstream 2-kb regions of genes and TEs. e Comparisons of relative gene expression levels (FPKM; fragments per kilobase of transcript per million mapped reads) of PpyDML1.1, PpyDML1.2, and PpyDML1.3 in the wild, landrace, and improved pear populations. PpyDML1.1, PpyDML1.2, and PpyDML1.3 showed continuous decreases in expression during pear domestication and improvement (*P < 0.05; **P < 0.01; ***P < 0.001, differentially expressed analysis using cuffdiff)