**5. Conclusions**

In summary, we used transcriptome approaches to study the molecular mechanism of petal coloration of four varieties of *R. pulchrum*. Our results show that variation in the flower color was related to the expression level of anthocyanin biosynthesis genes. The higher expression levels of genes associated with FLS might be the key to white formation, leading to more dihydroflavonol entering the flavonols branch. The formation of red color may be related to the higher expression of DFR genes, which promoted the accumulation of anthocyanin. The structural genes and their regulators (TFs) in this research provided valuable molecular information on the flower color intensity variation in *R. pulchrum*.

**Supplementary Materials:** The following are available online at https://www.mdpi.com/article/10 .3390/plants12142656/s1. Figure S1: The distribution and number of DEGs in three main categories in the three pairwise comparisons; Figure S2: Enrichment of top 10 GO pathways; Figure S3: GO enrichment analysis of DEGs in the three pairwise comparison groups; Figure S4: Distribution of the genes involved in phytohormone metabolic pathways in the three pairwise comparisons. Table S1: The contents of anthocyanin components; Table S2: Primer sequences of genes used in qRT-PCR validation; Table S3: Significantly enriched GO terms in the three pairwise comparison groups; Table S4: Genes involved in the anthocyanin biosynthesis pathway showing genotypic difference expression; Table S5: List of differentially expressed TFs identified in the three pairwise comparisons; Table S6: List of phytohormone signal-transduction- and biosynthesis-related DEGs.

**Author Contributions:** Conceptualization, N.Z. and C.Z.; methodology, C.Z.; software, N.Z.; validation, C.Z.; formal analysis, N.Z.; writing—original draft preparation, N.Z.; writing—review and editing, C.Z.; project administration, C.Z. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by Jiangsu Modern agricultural industrial technology system construction project, grant number JATS [2022] 489.

**Data Availability Statement:** The data is contained within the article and Supplementary Materials.

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