*2.3. Levels of mC Variation in Different Colored Petal Tissues*

The status and level of DNA methylation can vary between different individuals, tissues, and even genomic regions. We therefore explored variation in methylation between WT and RT samples in chromosomes as well as genomic regions. As shown in Figure 3b, the majority of strongly and weakly methylated regions occurred at similar chromosomal positions between the two samples. Calculated mCG/CG, mCHG/CHG, and mCHH/CHH ratios in the RT sample were 2.3–85%, 1.7–59%, and 0.4–4.3%, respectively. Many mC loci in RT were different from those in WT, where the mCG/CG, mCHG/CHG, and mCHH/CHH ratios were 2.8–83%, 1.7–61%, and 0.6–5%, respectively.

Although methylation levels in different genomic functional domains were higher in WT than in RT, they followed similar trends, with the highest and lowest methylation context ratios corresponding to mCG/CG and mCHH/CHH, respectively (Figure 3c). In the context of CG, methylation levels in exon and intron regions were higher than in promoter regions, but lower than in TE regions. For CHG and CHH, mCHG/CHG and mCHH/CHH ratios were lower in exon and intron regions than in promoter and transcriptional end site (TES) regions, although the difference in the mCHH/CHH ratio across various regions was not very pronounced. The highest methylation levels within gene bodies were at CG sites, whereas methylation levels in the ~2-kb upstream and downstream regions were highest at the CHG sites (Figure 3d). The lowest methylation levels, including at CG and CHG sites, were observed within regions adjacent to transcriptional start sites (TSSs) and TESs.

**Figure 3.** Epigenomic landscape and distribution of DNA methylation in white petal tissues (WT) and red petal tissues (RT) of *Prunus mume*. (**a**) Circos plots of chromosomes in *P. mume* WT and RT samples. The track order (from outside to inside) is as follows: (1–3) methylation density by sequence context (mCG, mCHG, and mCHH); (4) transposable element (TE) density; (5) gene density; and (6) number of reads generated by transcriptome sequencing. (**b**) Circos plots of differences in DNA methylation levels by methylation context (mCG, mCHG, and mCHH) in WT (outer track) and RT (inner track) genomes. The middle track in each plot indicates the degree of DNA methylation-level differences. (**c**) Distribution of DNA methylation levels within gene functional regions. The *x* and *y*-axes indicate gene functional domains and methylation levels, respectively. (**d**) Distribution of DNA methylation levels within gene-body domains and 2-kb upstream and downstream regions (TSS, transcriptional start site; TES, transcriptional end site). The *x* and *y*-axes indicate gene functional domains and methylation levels, respectively.
