Single-cell transcriptome atlas of Panax notoginseng embryonic shoot apex: Insights into developmental regulation and triterpene saponin biosynthesis

Panax notoginseng , a renowned medicinal herb, accumulates high levels of triterpene saponins, with its secondary metabolites being essential for cardio-cerebrovascular protective effects. While most transcriptome studies have identified key genes involved in developmental regulation and secondary metabolism of P. notoginseng , the spatial and cell-type-specific transcriptional regulation underlying both shoot apex organogenesis and saponins biosynthesis remains unresolved. This knowledge gap primarily stems from the limitations of bulk transcriptomics, which obscures cell-type heterogeneity and spatially restricted regulatory mechanisms. In this study, we constructed the first single-cell transcriptome atlas of the P. notoginseng embryonic shoot apex, resolving 14 transcriptionally distinct subclusters across seven major cell types. Developmental trajectory analysis revealed stage-specific transcriptional programs, with PAMP-triggered immunity-5 ( PTI5 ) and indeterminate-domain 12 ( IDD12 ) emerging as pivotal regulators during early meristematic differentiation. Spatial mapping of saponins biosynthetic pathways identified epidermal and mesophyll cells as primary sites for saponins accumulation, coordinated by cell-type-specific transcription factor families ( NAC , bHLH , MYB , ERF ). This study provides the first systematic framework for understanding how cell-type-specific transcriptional networks orchestrate both developmental trajectory and metabolic specialization in P. notoginseng . These insights not only advance the genetic engineering of high-yielding triterpene saponins cultivars but also establish a paradigm for studying secondary metabolism in non-model medicinal plants. • A single-cell transcriptome atlas of the embryonic shoot apex of P. notoginseng was constructed. • Detailed single-cell transcriptome analysis revealed cellular diversity and developmental trajectories. • Identification of transcription factors PTI5 and IDD12 crucial for early development. • Discovery of gene families and transcription factors regulating triterpene saponin production. • The study will promoting sustainable development of the P. notoginseng industry.