Multi-Omics Integration Reveals Organ-Specific Biosynthesis of Flavonoids and Terpenoids in the Medicinal Plant Bidens alba

Zhaochu Wang¹Xinyu Xu^2,3Peilan Zhang⁴Ye Huang²Chenzi Zhao¹Yousry A. El-Kassaby³Yangtao Chen¹Jing Wang^1*Rong Shi^1*

• ¹The Affiliated People’s Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
• ²College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
• ³The University of British Columbia Department of Forest & Conservation Sciences, Vancouver, Canada
• ⁴School of Tropical Agriculture and Forestry, Hainan University, Haikou, China

Bidens alba is a traditional medicinal plant with notable antioxidant, anti-inflammatory, and antimicrobial properties, largely attributed to its flavonoid and terpenoid constituents. However, the tissue-specific distribution and regulatory mechanisms of these metabolites remain unclear. Here, we integrated reference-guided transcriptomics and widely targeted metabolomics across four tissues (flowers, leaves, stems, and roots) to investigate the biosynthesis and accumulation of flavonoids and terpenoids in B. alba (Bidens alba). A total of 774 flavonoids and 311 terpenoids were identified, with flavonoids enriched in aerial parts and certain sesquiterpenes and triterpenes accumulating in roots. Transcriptome profiling revealed that genes such as CHS, F3H, FLS, HMGR, FPPS, and GGPPS exhibited tissue-specific expression consistent with metabolite patterns. Furthermore, we identified several candidate transcription factors, including BpMYB1, BpMYB2, and BpbHLH1, involved in regulating flavonoid biosynthesis, with BpMYB2 and BpbHLH1 showing opposing expression patterns in flowers and leaves. Terpenoid-related genes BpTPS1, BpTPS2, and BpTPS3 are putative regulators of GPPS, DXR, and other key enzymes, with BpTPS2/3 highly expressed in flowers. These findings reveal the transcriptional and metabolic basis of tissue-specific secondary metabolism in B. alba and provide valuable targets for functional validation and medicinal development.