Abstract

Introduction Canavalia gladiata ( C. gladiata ) is an important medicinal and edible plant. However, systematic research on the distribution of metabolites in different tissues of C. gladiata and their potential transcriptional regulatory mechanisms remain poorly understood. Methods We performed integrated metabolomic and transcriptomic analyses across five tissues (roots, stems, leaves, seeds, and fruit pericarps) of C. gladiata , combined with antioxidant capacity and bioactive component content assays, to dissect the regulatory networks of flavonoid and terpenoid biosynthesis. Results Seeds exhibited the highest antioxidant activity and total phenolic content, whereas leaves accumulated the highest levels of total flavonoids and terpenic acids. A total of 4,405 DAMs and 25,597 DEGs were identified, revealing pronounced tissue-specific metabolic and transcriptional divergence. Flavonoid and terpenoid biosynthesis pathways were significantly enriched in comparisons between seeds and other tissues. Key structural genes, including 4CL, CHS, FLS, HMGR , and DXS , displayed strong tissue-specific expression patterns. Co-expression network analysis identified candidate regulatory modules, highlighting MYB , bHLH , and MYC2 transcription factors as central regulators of flavonoid and terpenoid metabolism in seeds and fruit pericarps. Discussion This study provides the first comprehensive landscape of tissue-specific flavonoid and terpenoid metabolism in C. gladiata , offering a theoretical foundation and valuable genetic resources for the targeted exploitation of its bioactive components and molecular breeding.