Medicinal plants synthesize an immense diversity of specialized metabolites that play crucial roles in ecological interactions and serve as valuable pharmaceutical resources. However, the biosynthetic pathways responsible for this chemical diversity remain largely uncharacterized. These pathways are often complex, involving multiple steps that are spatially and temporally orchestrated within highly specialized or rare cell types. Classical bulk omics approaches obscure such cellular heterogeneity by averaging signals across tissues, limiting their utility in resolving cell-specific metabolic processes. Recent advances in single-cell and spatial omics technologies have revolutionized the ability to investigate plant metabolism at high spatiotemporal resolution, as exemplified by monoterpene indole alkaloids and Taxol biosynthesis. In this review, we highlight key technological advances in plant single-cell and spatial omics, examine their applications in pathway discovery and partitioning, and discuss emerging directions for harnessing these tools in plant synthetic biology and metabolic engineering. These developments promise to accelerate the systemic mapping of plant metabolic networks and facilitate their biotechnological exploitation for pharmaceutical development.

Medicinal plant  /  Single-cell omics  /  Specialized metabolite  /  Biosynthesis  /  Spatial transcriptomics  /  Metabolic compartmentation  /  Synthetic biology  /  Pharmaceutical development