Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species

Abstract Genomic structural variations (SVs) are widespread in plant and animal genomes and play important roles in phenotypic novelty and species adaptation. Frequent whole genome duplications followed by (re)diploidizations have resulted in high diversity of genome architecture among extant species. In this study, we identified abundant genomic SVs in the Panax genus that are hypothesized to have occurred through during the repeated polyploidizations/(re)diploidizations. Our genome‐wide comparisons demonstrated that although these polyploidization‐derived SVs have evolved at distinct evolutionary stages, a large number of SV‐intersecting genes showed enrichment in functionally important pathways related to secondary metabolites, photosynthesis and basic cellular activities. In line with these observations, our metabolic analyses of these Panax species revealed high diversity of primary and secondary metabolites both at the tissue and interspecific levels. In particular, genomic SVs identified at ginsenoside biosynthesis genes, including copy number variation and large fragment deletion, appear to have played important roles in the evolution and diversification of ginsenosides. A further herbivore deterrence experiment demonstrated that, as major triterpenoidal saponins found exclusively in Panax , ginsenosides provide protection against insect herbivores. Our study provides new insights on how polyploidization‐derived SVs have contributed to phenotypic novelty and plant adaptation.