Abstract
BACKGROUND: Sophora tonkinensis Gagnep is a significant Chinese herbal medicine, primarily composed of alkaloids and flavonoids, which are its key pharmacological components. Despite its importance, the metabolic pathways of these substances in S. tonkinensis remain inadequately explored. RESULTS: This study investigates the molecular regulation of alkaloid and flavonoid accumulation in S. tonkinensis. Through high-throughput transcriptome sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS) of seeds, leaves, stems, and roots, the research identifies differential metabolites and genes involved in alkaloid and flavonoid biosynthesis. The transcriptome analysis reveals 2,727 differentially expressed genes (DEGs), with 35 related to alkaloids and 48 to flavonoids. Metabolome analysis uncovers 296 differentially accumulated metabolites (DAMs), including 23 alkaloid-related DAMs and 23 flavonoid-related DAMs. Additionally, weighted gene co-expression network analysis suggests StCAO (evm. MODEL: 3.924) as a key regulator of alkaloid biosynthesis and StCHIs (evm. MODEL: 3.2047, evm. MODEL: 1.2104, and evm. MODEL: 1.2101) as crucial genes for flavonoid biosynthesis. To validate these findings, qPCR validation confirmed the consistency of expression trends for 12 selected DEGs across the roots, stems, leaves, and seeds of S. tonkinensis. CONCLUSION: This study offers a comprehensive analysis of the regulatory mechanisms governing alkaloid and flavonoid accumulation, as well as the associated key genes, across various S. tonkinensis tissues. These findings pave the way for future research into the regulatory processes of alkaloids and flavonoids in S. tonkinensis.