Fig. 2

Comparisons of differentially methylated regions (DMRs) in the wild vs. landrace and landrace vs. improved populations. Principal component analysis (PCA) plots of DNA methylation levels in the CG (a) and CHG (b) contexts. The yellow squares represent the wild pear accessions, the blue points represent the landrace pear accessions, and the green triangles represent the improved pear accessions. c The number of hyper/hypo-DMRs in the wild vs. landrace, landrace vs. improved, and wild vs. improved comparisons. d The total lengths of hyper/hypo-DMRs in the wild vs. landrace, landrace vs. improved, and wild vs. improved comparisons. e Comparisons of the lengths of DNA sequence regions under selection (DSRs) and the CG and CHG context DMRs in the wild vs. landrace and landrace vs. improved comparisons (*P < 0.05; **P < 0.01; ***P < 0.001, two-tailed paired Student’s t-test). f Genomic compositions of the DSRs and DMRs, including TEs, introns, exons, and intergenic regions. g Distribution of the DMRs between the wild and landrace populations for the 17 pear chromosomes. Proceeding from the outer ring to the inner ring, the data represents TE density (I), gene density (II), dom-CG-DMR density (III), dom-CHG-DMR density (IV), imp-CG-DMR density (V), imp-CHG-DMR density (VI), dom-DSR (VII), and imp-DSR (VIII). h Overlap of DMRs in the wild vs. landrace and landrace vs. improved comparisons for the CG and CHG contexts. i Overlap of DMRs in the 2 methylation contexts in the wild vs. landrace (domestication process) and landrace vs. improved (improvement process) comparisons. Correlation analysis between methylation levels of the CG and CHG contexts in o_CG_CHG_DMRs during pear domestication (j) and improvement (k)