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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 Van de Peer (UGent) , et al.
(2022) NATURE COMMUNICATIONS. 13(1).
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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. The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
Keywords
General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, GINSENOSIDE BIOSYNTHESIS, EVOLUTIONARY SIGNIFICANCE, HI-C, POLYPLOIDY, PROTOPANAXADIOL, PLASTICITY, CATALYZES, ALIGNMENT, INSIGHTS, PROVIDES

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MLA
Wang, Zhen-Hui, et al. “Reshuffling of the Ancestral Core-Eudicot Genome Shaped Chromatin Topology and Epigenetic Modification in Panax.” NATURE COMMUNICATIONS, vol. 13, no. 1, 2022, doi:10.1038/s41467-022-29561-5.
APA
Wang, Z.-H., Wang, X.-F., Lu, T., Li, M.-R., Jiang, P., Zhao, J., … Li, L.-F. (2022). Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. NATURE COMMUNICATIONS, 13(1). https://doi.org/10.1038/s41467-022-29561-5
Chicago author-date
Wang, Zhen-Hui, Xin-Feng Wang, Tianyuan Lu, Ming-Rui Li, Peng Jiang, Jing Zhao, Si-Tong Liu, et al. 2022. “Reshuffling of the Ancestral Core-Eudicot Genome Shaped Chromatin Topology and Epigenetic Modification in Panax.” NATURE COMMUNICATIONS 13 (1). https://doi.org/10.1038/s41467-022-29561-5.
Chicago author-date (all authors)
Wang, Zhen-Hui, Xin-Feng Wang, Tianyuan Lu, Ming-Rui Li, Peng Jiang, Jing Zhao, Si-Tong Liu, Xue-Qi Fu, Jonathan F. Wendel, Yves Van de Peer, Bao Liu, and Lin-Feng Li. 2022. “Reshuffling of the Ancestral Core-Eudicot Genome Shaped Chromatin Topology and Epigenetic Modification in Panax.” NATURE COMMUNICATIONS 13 (1). doi:10.1038/s41467-022-29561-5.
Vancouver
1.
Wang Z-H, Wang X-F, Lu T, Li M-R, Jiang P, Zhao J, et al. Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. NATURE COMMUNICATIONS. 2022;13(1).
IEEE
[1]
Z.-H. Wang et al., “Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax,” NATURE COMMUNICATIONS, vol. 13, no. 1, 2022.
@article{8751565,
  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.

The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.}},
  articleno    = {{1902}},
  author       = {{Wang, Zhen-Hui and Wang, Xin-Feng and Lu, Tianyuan and Li, Ming-Rui and Jiang, Peng and Zhao, Jing and Liu, Si-Tong and Fu, Xue-Qi and Wendel, Jonathan F. and Van de Peer, Yves and Liu, Bao and Li, Lin-Feng}},
  issn         = {{2041-1723}},
  journal      = {{NATURE COMMUNICATIONS}},
  keywords     = {{General Physics and Astronomy,General Biochemistry,Genetics and Molecular Biology,General Chemistry,GINSENOSIDE BIOSYNTHESIS,EVOLUTIONARY SIGNIFICANCE,HI-C,POLYPLOIDY,PROTOPANAXADIOL,PLASTICITY,CATALYZES,ALIGNMENT,INSIGHTS,PROVIDES}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{12}},
  title        = {{Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax}},
  url          = {{http://dx.doi.org/10.1038/s41467-022-29561-5}},
  volume       = {{13}},
  year         = {{2022}},
}
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