Molecular insights into the regulation of flower Coloration in Vernicia fordii through transcriptome and pigment analysis

• Integrated metabolomic and transcriptomic analyses of Vernicia fordii flowers. • 1212 metabolites identified, mainly from flavonoid and phenylpropanoid pathways. • Red flowers (‘WV’) accumulate glycosylated and acylated anthocyanins for stability. • Yellow flowers (‘YV’) show higher flavonol and flavone levels but reduced anthocyanins. Flower color is a key ornamental trait, yet the molecular basis of coloration in tung tree ( Vernicia fordii ), an economically important subtropical species, remains unclear. To elucidate the mechanisms underlying color differentiation, we integrated metabolomic and transcriptomic analyses of yellow-flowered (‘YV’) and red-flowered (‘WV’) tung trees. A total of 1212 metabolites and numerous differentially expressed genes (DEGs) were identified, revealing that flower pigmentation is primarily governed by the flavonoid and phenylpropanoid pathways. Red flowers (‘WV’) accumulated abundant glycosylated and acylated anthocyanins, conferring stable red coloration, whereas yellow flowers (‘YV’) showed reduced anthocyanin levels but increased accumulation of flavonol glycosides (e.g., 3- O -methylquercetin) and flavones (e.g., jaceosidin), resulting in yellow hues. Transcriptomic profiling indicated that CHS, CHI , and FLS were upregulated in ‘YV’, directing flux toward flavonol synthesis, while enhanced expression of PAL, 4CL, F3H, F3’H, DFR , and ANS in ‘WV’ favored anthocyanin biosynthesis. These coordinated metabolic and transcriptional shifts demonstrate that flower color divergence in V. fordii arises from differential allocation within the flavonoid pathway. This study not only provides the first comprehensive molecular framework of pigment formation in tung tree but also offers valuable targets for molecular breeding and biotechnological improvement of ornamental traits in woody plants.