Deciphering Alkaloid and Flavonoid Biosynthesis in Different Tissues of Sophora tonkinensis via Transcriptomics and Metabolomics

Abstract Background：Sophora tonkinensis Gagnep is an important Chinese herbal medicine, with alkaloids and flavonoids being the primary pharmacological substances. However, theinformation on the metabolic pathways of alkaloids and flavonoids in S. tonkinensis are not well understood. Results: This research delves into the molecular regulation of the accumulation of alkaloids and flavonoids in S. tonkinensis. By examining four tissues (seeds, leaves, stems, and roots), through high-throughput transcriptome sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS), it identified differential metabolites and genes related to alkaloid and flavonoid biosynthesis. Transcriptome analysis identified 2,727 differentially expressed genes (DEGs). Among these DEGs, 35 were related to alkaloids and 48 to flavonoids. Furthermore, metabolome analysis revealed 296 differentially expressed metabolites (DEMs), comprising 23 alkaloid-related DEMs and 23 flavonoid-related DEMs. Additionally, the weighted gene co-expression network analysis highlighted the potential of StCAO (evm.model.3.924) in regulating alkaloid biosynthesis and StCHIs (evm.model.3.2047, evm.model.1.2104, and evm.model.1.2101) in flavonoid biosynthesis. To reinforce 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 provides a detailed exploration of the regulatory mechanisms of alkaloid and flavonoid accumulation and associated key genes in different S. tonkinensis tissues. These findings provide insights for future investigations into the regulatory mechanisms of alkaloids and flavonoids in S. tonkinensis.