Omics-based profiling and therapeutic potential of natural components in pan-Shennongjia medicinal herbs

The pan-Shennongjia region represents a globally significant biodiversity hotspot characterized by high species diversity and endemism. While its rich medicinal resources have long been recognized, the systematic characterization of their natural components and therapeutic potential remains underexplored. Here, we integrated 405 representative biological species from the pan-Shennongjia region, corresponding to 323 traditional Chinese medicine materials, into a Chinese genus-species level phylogenetic tree. We identified clade-specific species enrichments at the family level within this region. Notably, case studies of Chrysanthemum indicum var. aromaticum and Dendrobium flexicaule and Chrysanthemum indicum var. aromaticum revealed specificized accumulations of polysaccharides and volatile terpenoids, respectively, suggesting an environmentally-driven adaptive diversification of metabolomic profiles in pan-Shennongjia herbs. To comprehensively characterize this, we constructed a pan-Shennongjia Herbs Multi-Omics Components (SHMC) database, integrating over 20 million diverse omics-based molecules including small RNAs, small peptides, secondary metabolites, and carbohydrates. Analysis of the components distribution patterns across species revealed phylogenetic selectivity. To validate the accuracy of the annotated components, we systematically analyzed secondary metabolites and small RNAs in Coptis chinensis, and small peptides in Scolopendra subspinipes mutilans based on additional transcriptomic and metabolomic data, and further evaluated their therapeutic potential. This study establishes a crucial foundation for the conservation and sustainable utilization of pan-Shennongjia's medicinal resources, offering the first regional-scale omics-based component database for mining valuable natural products.