Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family

Ren-Gang Zhang, Hang Zhao, Justin L. Conover, Hong-Yun Shang, Liu De-Tuan, Min-Jie Zhou, Xiong-Fang Liu, Kai-Hua Jia, Shi-Cheng Shao, Meng-Meng Li, Chong-Yang Jin, Yi-Hui Liu, Xiao-Yi Shen, Da-Wei Li (), Martin A. Lysak (), Jonathan F. Wendel (), Xiao-Yang Ge () and Yong-Peng Ma ()
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Ren-Gang Zhang: Chinese Academy of Sciences
Hang Zhao: Chinese Academy of Agricultural Sciences
Justin L. Conover: University of Arizona
Hong-Yun Shang: Chinese Academy of Sciences
Liu De-Tuan: Chinese Academy of Sciences
Min-Jie Zhou: Chinese Academy of Sciences
Xiong-Fang Liu: Chinese Academy of Sciences
Kai-Hua Jia: Shandong Academy of Agricultural Sciences
Shi-Cheng Shao: Chinese Academy of Sciences
Meng-Meng Li: Chinese Academy of Agricultural Sciences
Chong-Yang Jin: Chinese Academy of Agricultural Sciences
Yi-Hui Liu: Qufu Normal University
Xiao-Yi Shen: Chinese Academy of Agricultural Sciences
Da-Wei Li: Chinese Academy of Sciences
Martin A. Lysak: Masaryk University
Jonathan F. Wendel: Iowa State University
Xiao-Yang Ge: Chinese Academy of Agricultural Sciences
Yong-Peng Ma: Chinese Academy of Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract Polyploidy and subsequent post-polyploid diploidization (PPD) are key drivers of plant genome evolution, yet their contributions to evolutionary success remain debated. Here, we analyze the Malvaceae family as an exemplary system for elucidating the evolutionary role of polyploidy and PPD in angiosperms, leveraging 11 high-quality chromosome-scale genomes from all nine subfamilies, including newly sequenced, near telomere-to-telomere assemblies from four of these subfamilies. Our findings reveal a complex reticulate paleoallopolyploidy history early in the diversification of the Malvadendrina clade, characterized by multiple rounds of species radiation punctuated by ancient allotetraploidization (Mal-β) and allodecaploidization (Mal-α) events around the Cretaceous–Paleogene (K–Pg) boundary. We further reconstruct the evolutionary dynamics of PPD and find a strong correlation between dysploidy rate and taxonomic richness of the paleopolyploid subfamilies (R2 ≥ 0.90, P

Date: 2025
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DOI: 10.1038/s41467-025-62644-7

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