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 KeYou 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 Van de Peer, Zhong Jian Liu

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


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.

Original languageEnglish
Article number3661
JournalNature communications
Issue number1
Publication statusPublished - 2023 Dec

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • General Biochemistry,Genetics and Molecular Biology
  • General Physics and Astronomy


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