Multi-omics integration reveals organ-specific biosynthesis of flavonoids and terpenoids in the medicinal plant Bidens alba

Introduction Bidens alba is a traditional medicinal plant valued for its antioxidant, anti-inflammatory, and antimicrobial properties, largely attributed to flavonoids and terpenoids. However, the tissue-specific distribution and regulatory mechanisms of these metabolites remain poorly understood. Methods We employed a combined approach of reference-guided transcriptomics and widely targeted metabolomics to investigate the biosynthesis and accumulation of flavonoids and terpenoids in four tissues (flowers, leaves, stems, and roots) of B. alba . Results A total of 774 flavonoids and 311 terpenoids were identified. Flavonoids were enriched in aerial tissues, while certain sesquiterpenes and triterpenes accumulated in roots. Transcriptome profiling revealed tissue-specific expression of key biosynthetic genes, including CHS, F3H, FLS, HMGR, FPPS , and GGPPS , which corresponded with metabolite patterns. Several transcription factors, such as BpMYB1, BpMYB2 , and BpbHLH1 , were identified as candidates regulating flavonoid biosynthesis, with BpMYB2 and BpbHLH1 showing contrasting expression between flowers and leaves. For terpenoid biosynthesis, BpTPS1, BpTPS2 , and BpTPS3 were identified as putative regulators of enzymes including GPPS and DXR , with BpTPS2/3 highly expressed in flowers. Discussion These findings provide new insights into the transcriptional and metabolic basis of tissue-specific secondary metabolism in B. alba . The identified candidate genes and regulatory factors represent valuable targets for future functional validation and hold potential for medicinal development and molecular breeding of this species.