Integrated Transcriptomic and Metabolomic Analysis Identified Key Transcriptional Factors Involved in Flavonoid and Alkaloid Biosynthesis Among Different Tissues of Sophora flavescens

Sophora flavescenshas anti-inflammatory, analgesic, antibacterial, antiviral, and anti-tumor properties due to its active compounds, including alkaloids and flavonoids. Exploring the biosynthetic regulation mechanism of these compounds is crucial. Here, we identified 227 flavonoids and 55 alkaloids among five tissues (roots, stems, leaves, flowers, and pods) using wide-targeted metabolomics. Flavonoids were predominantly in roots, whereas alkaloids were primarily in roots and flowers. RNA sequencing revealed 18,488 differentially expressed genes (DEGs) in non-root tissues compared to roots. These DEGs were significantly enriched in pathways such as plant hormone signal transduction, carbon metabolism, flavonoid biosynthesis, and isoflavonoid biosynthesis. Utilizing K-means clustering and WGCNA, we identified ten transcription factors (TFs) potentially regulating the biosynthesis and accumulation of flavonoids (e.g., SfWRKY50 and SfbHLH078) and seven TFs involved in alkaloid biosynthesis (e.g., SfbHLH109 and SfbHLH162) inS. flavescens. These TFs can serve as candidate genes for studying the biosynthetic mechanisms of flavonoids and alkaloids, providing insights into the production of key active compounds and supporting the rational use ofS. flavescenstissues.