Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

Zhen-Hui Wang, Xin-Feng Wang, Tianyuan Lu, Ming-Rui Li, Peng Jiang, Jing Zhao, Si-Tong Liu, Xue-Qi Fu, Jonathan F. Wendel, Yves Peer (), Bao Liu () and Lin-Feng Li ()
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Zhen-Hui Wang: Jilin Agricultural University
Xin-Feng Wang: Fudan University
Tianyuan Lu: McGill University and Genome Quebec Innovation Center
Ming-Rui Li: Fudan University
Peng Jiang: Northeast Normal University
Jing Zhao: Northeast Normal University
Si-Tong Liu: Jilin University
Xue-Qi Fu: Jilin University
Jonathan F. Wendel: Iowa State University
Yves Peer: Ghent University and VIB Center for Plant Systems Biology
Bao Liu: Northeast Normal University
Lin-Feng Li: Fudan University

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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 paleo-polyploidization 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.

Date: 2022
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DOI: 10.1038/s41467-022-29561-5

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