A CcMYB90-CcCHS1 module regulates flavonoid biosynthesis during pericarp darkening in Cinnamomum camphora

In the camphor tree ( Cinnamomum camphora L.), bioactive metabolites are found in different parts, including the leaves, fruits, and stems; its fruit, particularly the pericarp, is abundant in flavonoids and volatile compounds. However, mechanisms regulating the changes in pericarp color during fruit maturation remain unclear in this species. Therefore, we investigated the molecular basis of pericarp coloration in C. camphora by profiling metabolites and transcripts from the immature to the fully mature stage (green to dark; P1-P4). Targeted metabolomic profiling identified 618 differentially accumulated flavonoid metabolites across the four stages, among which delphinidin-3-O-glucoside, cyanidin-3-O-glucoside, and pelargonidin-3-O-glucoside were strongly associated with pericarp darkening. Transcriptome analysis revealed that MYB was the largest group of transcription factors (TFs) associated with pericarp darkening, with CcMYB90 showing the highest expression. CcMYB90 expression varied dramatically during pericarp darkening. In addition, CcCHS1 , a structural gene encoding chalcone synthase and associated with anthocyanin accumulation, was identified as a direct downstream target of CcMYB90. Overexpression of CcMYB90 in Arabidopsis thaliana upregulated genes involved in anthocyanin synthesis, consequently increasing anthocyanin levels. In vitro and in planta assays further demonstrated that CcMYB90 binds to the CcCHS1 promoter, enhances its expression, and thereby activates flavonoid synthesis. Together, these findings support a proposed role for the CcMYB90-CcCHS1 module in flavonoid and anthocyanin biosynthesis and pericarp darkening during C. camphora fruit maturation.