Ancient allopolyploidy and specific subgenomic evolution drove the radiation of poplars and willows

Deyan Wang, Mengmeng Li, Wenlu Yang, Kai Chen, Jiale Zhao, Lanxing Shan, Pengchuan Sun, Li Xu, Zhiqiang Lu, Yiling Li, Yang Chen, Jiaxiao Xie, Yubo Wang, Heng Huang, Ao Feng, Xiaoning Hao, Tiannan Luo, Jianglin Luo, Yuanzhong Jiang, Quanjun Hu, Zhenxiang Xi, Jianquan Liu (), Matthew Olson () and Tao Ma ()
Additional contact information
Deyan Wang: Sichuan University
Mengmeng Li: Sichuan University
Wenlu Yang: Sichuan University
Kai Chen: Sichuan University
Jiale Zhao: Sichuan University
Lanxing Shan: Sichuan University
Pengchuan Sun: Sichuan University
Li Xu: Sichuan University
Zhiqiang Lu: Chinese Academy of Sciences
Yiling Li: Sichuan University
Yang Chen: Sichuan University
Jiaxiao Xie: Sichuan University
Yubo Wang: Sichuan University
Heng Huang: Sichuan University
Ao Feng: Sichuan University
Xiaoning Hao: Sichuan University
Tiannan Luo: Sichuan University
Jianglin Luo: Sichuan University
Yuanzhong Jiang: Sichuan University
Quanjun Hu: Sichuan University
Zhenxiang Xi: Sichuan University
Jianquan Liu: Sichuan University
Matthew Olson: Texas Tech University
Tao Ma: Sichuan University

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

Abstract: Abstract Allopolyploidy involves the fusion of genomes from different lineages through hybridization and chromosome doubling. However, detecting early allopolyploidy events and understanding the specific subgenomic evolution that contributes to the origin of adaptive innovations for species radiation can be challenging. Here, we present genomes representing all three subfamilies of Salicaceae, a woody model clade, and collect epigenetic and transcriptomic samples. We reveal one shared ancient allopolyploidy event involving Populus, Salix and two sister genera, followed by contrasted karyotypic and subgenomic evolution. The specific evolution sets the stage for the origin of novel photoperiod responses, flowering phenology and small-hairy seeds in the highly speciose Populus and Salix compared with their species-depauperate sister genera, which may lead to their ecological adaptation and radiation. Our findings underscore the role of ancient allopolyploidization and specific subgenomic evolution in driving both innovation and species diversification at deep nodes of the plant tree of life.

Date: 2025
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DOI: 10.1038/s41467-025-62178-y

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