Polyploidization driven pan-genome structural remodeling and gene duplication mediated functional diversification in Panax.

Polyploidization serves as a major driver of plant genome evolution and functional innovation. However, how it influences genome structural remodeling and functional divergence remains unclear. In this study, we selected six species with different ploidy levels in the genus Panax as research materials. By integrating pan-genome and gene duplication analyses, we systematically evaluated the evolutionary patterns under distinct ploidy backgrounds. The results showed that, under their respective ploidy-specific pan-genome frameworks, tetraploid species had a higher proportion of core genes than diploid species. This compositional difference, combined with extensive gene family remodeling in tetraploid lineages, suggests that polyploidization was accompanied by systematic genome structural reorganization, likely driven by distinct selective pressures corresponding to different modes of gene duplication. The composition of duplication types differed extremely significantly among ploidy levels, and WGD as well as TRD were significantly elevated in tetraploid species. Further analysis revealed that WGD contributed predominantly to core genes, whereas DSD and TRD were more involved in the formation of dispensable and private genes. Functional analysis indicated that duplicated genes in tetraploids were involved in a broader range of metabolic and cellular processes, among which private genes derived from DSD were significantly enriched in DNA replication and repair pathways. These findings suggest that polyploidization promotes functional diversification while maintaining core functional stability by regulating different duplication mechanisms, thereby driving genome structural reorganization and adaptive evolution in Panax. These findings provide a genomic framework for understanding the diversity of bioactive compounds and may support future breeding and quality improvement of Panax medicinal resources.