Integration of ATAC-seq and RNA-seq profiling reveals an epigenetic regulator of anthocyanin synthesis in Prunus mume

BACKGROUND: The flower color is the key ornamental trait of Prunus mume (Mei) with a cultivation history of over 3,000 years in East Asia. Although the genetic regulation of pigment biosynthesis of P. mume has been partially characterized, the impact of chromatin accessibility on color development remains elusive. RESULTS: To explore epigenetic mechanisms underlying anthocyanin synthesis, we utilized naturally color-varying cultivar P. mume 'Fuban Tiaozhi' as experimental material and conducted assays for transposase-accessible chromatin sequencing, RNA sequencing, and functional validation of candidate genes. Transcriptome analysis identified that 17 structural genes involved in anthocyanin biosynthesis and constructed this pathway map in P. mume. ATAC-seq analysis further revealed the number of genes with chromatin accessibility was significantly higher in TZH than in TZB. We identified 93 differentially accessible motifs between TZB and TZH, which include bHLH, bZIP, C2H2, CDF, and MYB. Integrated RNA-seq and ATAC-seq analysis revealed one structural gene (PmLDOX1) and five differentially expressed TFs (one bHLH and four MYB), including PmMYB308.1. Notably, the chromatin openness of PmMYB308.1 in TZH increased compared to TZB, while the expression level of the gene decreased. Overexpression of PmMYB308.1 in tobacco significantly suppressed anthocyanin accumulation. In addition, based on the above analysis, we propose a potential correlation between PmMYB308.1 and the PmLDOX1 promoter. CONCLUSIONS: Based on ATAC-seq and motif analysis, increased chromatin accessibility of genes involved in the regulation of anthocyanin biosynthesis may promote pigment accumulation in TZH. Moreover, the downregulation of the negative regulatory gene PmMYB308.1 may also be an important contributing factor to anthocyanin accumulation in TZH petals. The results provide novel insights into the epigenetic regulation of anthocyanin synthesis in P. mume and establish a theoretical foundation and screening targets for investigating color traits in Rosaceae and other woody ornamental plants via chromatin accessibility analysis.