Diploid and tetraploid genomes of Acorus and the evolution of monocots

Liang Ma, Ke-Wei Liu, Zhen Li, Yu-Yun Hsiao, Yiying Qi, Tao Fu, Guang-Da Tang, Diyang Zhang, Wei-Hong Sun, Ding-Kun Liu, Yuanyuan Li, Gui-Zhen Chen, Xue-Die Liu, Xing-Yu Liao, Yu-Ting Jiang, Xia Yu, Yang Hao, Jie Huang, Xue-Wei Zhao, Shijie Ke, You-Yi Chen, Wan-Lin Wu, Jui-Ling Hsu, Yu-Fu Lin, Ming- Der Huang, Chia-Ying Li, Laiqiang Huang, Zhi-Wen Wang, Xiang Zhao, Wen-Ying Zhong, Dong-Hui Peng, Sagheer Ahmad, Siren Lan (), Ji-Sen Zhang (), Wen-Chieh Tsai (), Yves Peer () and Zhong-Jian Liu ()
Additional contact information
Liang Ma: Fujian Agriculture and Forestry University
Ke-Wei Liu: Tsinghua University
Zhen Li: Ghent University
Yu-Yun Hsiao: National Cheng Kung University
Yiying Qi: Fujian Agriculture and Forestry University
Tao Fu: BGI Genomics, BGI-Shenzhen
Guang-Da Tang: Shaoguan University
Diyang Zhang: Fujian Agriculture and Forestry University
Wei-Hong Sun: Fujian Agriculture and Forestry University
Ding-Kun Liu: Fujian Agriculture and Forestry University
Yuanyuan Li: Fujian Agriculture and Forestry University
Gui-Zhen Chen: Fujian Agriculture and Forestry University
Xue-Die Liu: Fujian Agriculture and Forestry University
Xing-Yu Liao: Fujian Agriculture and Forestry University
Yu-Ting Jiang: Fujian Agriculture and Forestry University
Xia Yu: Fujian Agriculture and Forestry University
Yang Hao: Fujian Agriculture and Forestry University
Jie Huang: Fujian Agriculture and Forestry University
Xue-Wei Zhao: Fujian Agriculture and Forestry University
Shijie Ke: Fujian Agriculture and Forestry University
You-Yi Chen: National Cheng Kung University
Wan-Lin Wu: National Cheng Kung University
Jui-Ling Hsu: National Cheng Kung University
Yu-Fu Lin: National Cheng Kung University
Ming- Der Huang: National Sun Yat-sen University
Chia-Ying Li: National Pingtung University
Laiqiang Huang: Tsinghua University
Zhi-Wen Wang: PubBio-Tech
Xiang Zhao: PubBio-Tech
Wen-Ying Zhong: PubBio-Tech
Dong-Hui Peng: Fujian Agriculture and Forestry University
Sagheer Ahmad: Fujian Agriculture and Forestry University
Siren Lan: Fujian Agriculture and Forestry University
Ji-Sen Zhang: Fujian Agriculture and Forestry University
Wen-Chieh Tsai: National Cheng Kung University
Yves Peer: Ghent University
Zhong-Jian Liu: Fujian Agriculture and Forestry University

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.

Date: 2023
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DOI: 10.1038/s41467-023-38829-3

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