Metabolomic and Transcriptomic Profiling Reveals Tissue-Specific Distribution and Molecular Regulation of Bioactive Compounds in Marsdenia tenacissima

Marsdenia tenacissima (MT), has its stems officially documented in the Chinese Pharmacopoeia. It is rich in bioactive C21 steroidal saponins and flavonoids with demonstrated anti-tumor activity. Wild MT resources are currently depleted due to overharvesting, while the metabolic mechanisms and utilization potential of non-traditional medicinal parts remain unclear. Metabolomics profiling identified 1,766 metabolites, revealing distinct metabolic specializations among tissues: roots were enriched in terpenoids, leaves in flavonoids/phenolic acids, and stems in amino acids/derivatives. Chemical analysis further demonstrated tissue-specific distribution of C21 steroidal saponins: roots served as the primary synthesis/storage site for tenacigenin B-derived saponins (S2/S4 types), stems predominantly contained S3-type glycosylated variants, while leaves accumulated tenacigenin C aglycones. Multi-omics integration revealed: Root-specific activation of terpenoid backbone biosynthesis, with upregulated MVA pathway genes (HMGCS, AACT) and terpene synthases (GGPS, DPPS). Glycerol-3-phosphate (G3P) accumulation positively correlated with HDR expression, regulating steroidal precursor supply. Leaf-dominant flavonoid biosynthesis driven by upregulated ANR, DFR, and CCoAOMT genes, promoting accumulation of phloretin-2'-O-glucoside, 3,5,7-trihydroxyflavanone, and catechin. Notably, root tissues exhibited minimal endogenous flavonoid synthesis, potentially avoiding interference with root development. This study is the first to elucidate the molecular mechanisms underlying efficient steroidal saponin synthesis in MT roots and flavonoid biosynthesis dominance in leaves. These findings break the conventional stem-only usage paradigm and provide a theoretical foundation for whole-plant resource utilization of MT.