Transcriptome analysis reveals regulatory networks and hub genes in flavonoid metabolism of Rosa roxburghii

Rosa roxburghii Tratt, the most popular fruit that blooms in the southwest of China, is rich in flavonoids. However, the regulatory network and critical genes involved in the metabolism of flavonoid compounds in R. roxburghii are still unknown. In this study, we revealed that flavonoid, anthocyanin and catechin accumulated at different levels in various tissues of R. roxburghii. We further obtained and analyzed differentially expressed genes (DEGs) involved in flavonoid metabolism from five samples of R. roxburghii by transcriptome sequencing. A total of 1 130 DEGs were identified, including 166 flavonoid pathway biosynthesis genes, 622 transcription factors, 301 transporters, and 221 cytochrome P450 proteins. A weighted gene co-expression network analysis (WGCNA) of the DEGs uncovered different co-expression networks. In terms of biosynthesis enzymes, cytochrome P450 CYP749A22 and CYP72A219 were highlighted in regulation flavonoids content. Anthocyanin 3-O-glucosyltransferase and F3H were the top two critical enzymes for anthocyanin content. In contrast, caffeic acid 3-O-methyltransferase, 4-coumarate-CoA ligase, and shikimate O-hydroxycinnamoyl transferase were essential for catechin accumulation. Additionally, the eigengene network of the "black" module had high correlations with total flavonoid (r= 0.9, p=5e-06). There were 26 eigengenes in the "black" module, including six flavonoid biosynthesis, 14 TFs and six transporters. Among them, besides cytochrome P450 proteins (DN136557_c0_g1, DN135573_c0_g1 and DN145971_c4_g1), isoflavone-hydroxylase (DN143321_c3_g1) was crucial for total flavonoids content based on the high degree of connectivity. The transcription factors RrWRKY45 (DN142829_c1_g5), RrTCP20 (DN146443_c1_g1) and RrERF118 (DN141507_c3_g2) were significantly correlated with flavonoids in R. roxburghii. The present transcriptomic and biochemical data on metabolites should encourage further investigation on functional genomics and breeding of R. roxburghii with strong pharmaceutical potential.