Table S1. Details of the bisulfite sequencing libraries generated in the study. Table S2. Effective coverage of intergenic region. Table S3. Distribution of DMRs on chromosomes. Table S4. Summary of the sequencing data generated for RNA-Seq and mapping on the apple genome. Table S5. List of differentially expressed genes involved in the anthocyanin pathway in the three comparisons. Table S6. Average methylation level of five apple cultivars. Table S7. Primers for qRT-PCR and BS-PCR. (DOCX 34 kb)