Abstract:
All extant core-eudicot plants share a common ancestral genome that has experienced cyclic
polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome
generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical
genome architecture, such as chromatin topology and gene expression, remains poorly
understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid
Panax species and conduct in-depth comparative genomic and epigenomic analyses.
We show that chromosomal interactions within each duplicated ancestral chromosome
largely maintain in extant Panax species, albeit experiencing ca. 100–150 million years of
evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation
divergence during polyploidization/(re)diploidization processes generate remarkable biochemical
diversity of secondary metabolites in the Panax genus. Our study provides a paleopolyploidization
perspective of how reshuffling of the ancestral core-eudicot genome leads to
a highly dynamic genome and to the metabolic diversification of extant eudicot plants.
