Integration of transcriptome and metabolome provides new insights to flavonoid biosynthesis in Cinnamomum camphora

Flavonoids are not only widely applied in the food, pharmaceutical and cosmetic industries, but also possess diverse biological functions that play crucial roles in plant physiology, growth and development, and ecology. The camphor tree ( Cinnamomum camphora (L.)) holds significant economic and ecological value; however, its flavonoid composition and the underlying biosynthetic mechanisms remain largely unexplored. In this study, widely targeted metabolomics and transcriptomics were integrated to comprehensively analyze the leaves of C. camphora . The results revealed significant metabolic differences among fresh leaves of different C. camphora chemotype s . with both DAMs and DEGs being significantly enriched in the flavonoid biosynthesis pathway. Quercetin-5- O -glucuronide, rhamnetin-3- O -glucoside, juglanin, catechin and (-)-epicatechin were identified as the major DAMs. Furthermore, the key enzymes involved in the flavonoid biosynthetic pathway, such as PAL, C4H, and 4CL, CHS, CHI, F3H, FLS, DFR, ANS, LAR, C3H, and HCT were identified. Among these, CcC4H1 was identified as a hub gene in co-expression network. Compared with the control, transient overexpression of CcC4H1 significantly increased the total flavonoid content in C. camphora leaves by 1.45-fold (reaching 2.42 mg/g), while significantly elevating the flavonoids compounds such as 8-C-methylquercetin 3-xyloside, 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-[(2S,3S,4 R,5S,6 R)-2,3,5-trihydroxy-6-methyloxan-4-yl]oxychromen-4-one, and rhamnetin-3- O -glucoside, with increases ranging from 1.88- to 22.79-fold. These findings provide important insights into the molecular regulation mechanisms of flavonoid biosynthesis in camphor trees and provide important information for the selection of varieties rich in flavonoids. • Significant metabolic differences were observed in the fresh leaves of five chemical type camphor trees. • DEGs and DAMs were significantly enriched in flavonoid biosynthesis. • Quercetin-5- O -glucuronide, rhamnetin-3- O -glucoside, juglanin, catechin and epicatechin are the main DAMs. • Mining candidate genes in flavonoid biosynthesis by multiple omics analysis. • The CcC4H1 gene found to increase the accumulation of flavonoids in camphor tree leaves.