Combined Study of Transcriptome and Metabolome Reveals Involvement of Metabolites and Candidate Genes in Flavonoid Biosynthesis in Prunus avium L.

Sweet cherry (Prunus avium L.) is a popular fruit tree grown for its juicy fruit and pleasing appearance. The fruit pf the sweet cherry contains active antioxidants and other chemical compounds essential for human health. For this study, we performed the transcriptomics and metabolomics analysis using young Green Peel (GP) and mature Red Peel (RP) from sweet cherries to understand the underlying genetic mechanism regulating fruit development and ripening. Using high-throughput RNA sequencing and ultra-performance liquid chromatography, with quadrupole time-of-flight tandem mass spectrometry, respectively, metabolic and transcript profiling was obtained. Relative to GP, there were equal quantities of pronouncedly varied metabolites in RP (n = 3564). Differentially expressed genes (DEGs, n = 3564), containing 45 transcription factor (TF) families, were recorded in RP. Meanwhile, 182 differentially expressed TF (DETF) members of 37 TF families, were displayed in abundance in RP compared to GP sweet cherries. The largest quantities of DETFs were members of the ERF (25) and basic helix–loop–helix (bHLH) (19) families, followed by the MYB (18), WRKY (18), and C2H2 (12) families. Interestingly, most ERF genes were down-regulated, whereas CCCH genes were mainly up-regulated in RP. Other DETFs exhibited significant variations. In addition, RT-QPCR results and metabolomics data together with transcriptomic data revealed that the abundance of catechin, epicatechin, rhoifolin, myricetin, keracyanin, and the other six glycosyltransferase genes was highly increased in RP when compared to GP sweet cherries. The relatively higher expression of DETFs, metabolite, and flavonoid biosynthesis in RP sweet cherries suggests the accumulation of distinct metabolites that cause red coloring during fruit development and ripening. Thus, the metabolomics and transcriptomic analysis of the current study are powerful tools for providing more valuable information for the metabolic engineering of flavonoids biosynthesis in sweet cherries. They are also helpful in understanding the relationship between genotype and phenotype.