**5. Conclusions**

Flower color chimerism has since served as important material for landscaping application and genetic improvement. In our study, we detected the specific color substances, i.e., cyanidin 3,5-*O*-diglucoside, cyanidin 3-*O*-glucoside, and peonidin 3-*O*-glucoside, in red petal tissues of *P*. *mume* "Danban Tiaozhi". Simultaneously, we investigated the molecular mechanism of chimeric flowers by using a comparative methylomic–transcriptomic approach. We mapped the first-ever generated methylomes of *P*. *mume*, and determined that gene expression was negatively correlated with methylcytosine level in general and uncovered significant epigenetic variation between WT and RT. We also detected DMRs and DMR-related genes between WT and RT, and concluded that many of these genes, including DEGs and transcription factor genes, are critical participants in the anthocyanin regulatory pathway. Importantly, some of the associated DEGs harbored TE insertions that were also modified by methylcytosine. It suggests that flower color chimerism in *P*. *mume* is induced by the DNA methylation of critical genes and TEs.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/1422-0067/19/8/2315/s1.

**Author Contributions:** K.-F.M., Q.-X.Z. designed the experiments; T.-R.C., X.-L.Y., H.-T.P., and J.W. collected the plant materials and performed the qualitative and quantitative analysis on the content of anthocyanins; K.-F.M. did the experiment in molecular biology and analyzed the data profiles; K.-F.M. and Q.-X.Z. wrote the manuscript; T.-R.C., X.-L.Y., H.-T.P., and J.W. provided suggestions for manuscript revision.

**Funding:** This research was supported by the Fundamental Research Funds for the Central Universities (Nos. 2016ZCQ02 and BLX2013010), the National Natural Science Foundation of China (No. 31501787), and the Special Fund for Beijing Common Construction Project.

**Conflicts of Interest:** The authors declare no conflicts of interest.
