Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis

Sophora tonkinensis (shandougen) is a medicinal legume valued for its bioactive compound matrine, which has significant anti-inflammatory, antibacterial, and anticancer properties. In this study, we assembled a high-quality chromosomal-scale genome of S. tonkinensis and integrated transcriptome analysis under various abiotic stress conditions to investigate the molecular mechanisms underlying matrine biosynthesis. The genome of S. tonkinensis was sequenced to a size of 899 Mb with 95.9% completeness, revealing 37,930 protein-coding genes. Evolutionary analysis revealed two whole-genome duplication (WGD) events in S. tonkinensis. Transcriptomic profiling under drought stress treatments demonstrated that certain stress conditions upregulate key genes involved in the matrine biosynthesis pathway, suggesting that matrine accumulation may be modulated by environmental factors. Furthermore, we conducted a comprehensive analysis of the cytochrome P450 (CYP450) gene family, identifying 226 StCYP450 genes.These genes form multiple gene clusters and primarily originated from WGD and single-gene duplication events. They are likely involved in matrine biosynthesis and stress responses. Our findings provide valuable insights into the genetic and transcriptional basis of stress-induced matrine biosynthesis and offer foundational resources for future functional genomics studies in S. tonkinensis and other medicinal legumes.