Xu, Z.; Li, W.; Wei, F.-g.; Xiong, G.; Chen, Z.-j.; Gao, L.-z.

The medicinal herb Panax notoginseng produces a structurally diverse array of triterpene saponins (ginsenosides), yet the genetic basis of this chemical complexity remains unclear. Here we present a high quality chromosome level genome of diploid P. notoginseng and integrate comparative genomics with multi tissue, multi year metabolomics and transcriptomics. Surprisingly, unlike tetraploid Panax species, P. notoginseng shows no general expansion of core saponin biosynthetic gene families. Instead, lineage specific diversification of UDP glycosyltransferase (UGT) families, a recent burst of LTR retrotransposons, and enrichment of species specific genes in metabolic modification pathways point to an alternative evolutionary route. Saponin accumulation follows strict spatiotemporal compartmentalisation, and co expression network analysis reveals that the biosynthetic machinery is not static but continuously rewired during development -from a basic synthesis module in the first year to a modular pattern supporting both broad accumulation and branch specific modification by the third year. Seventeen differentially expressed UGTs show clear tissue preferences and saponin branch correlations. As a representative example, PnUGT33 is tightly linked to the PPD type saponin branch; structural modelling, molecular docking and 100 ns molecular dynamics simulations demonstrate its differential recognition of diverse triterpene skeletons. Collectively, our findings establish that ginsenoside diversity in diploid P. notoginseng arises primarily from UGT lineage diversification, developmentally rewired regulatory networks and UGT mediated branch selective post modification, rather than from expansion of core pathway genes. This work provides a new paradigm for understanding how plants achieve metabolic complexity without whole genome duplication or massive gene amplification.