Diploid and tetraploid genomes of Acorus and the evolution of monocots
Liang Ma, Kewei Liu, Zhen Li, Yu‐Yun Hsiao, Yiying Qi, Tao Fu, Guangda Tang, Diyang Zhang, Weihong Sun, Ding‐Kun Liu, Yuanyuan Li, Gui-Zhen Chen, Xuedie Liu, Xing‐Yu Liao, Yu-Ting Jiang, Xia Yu, Hao Yang, Jie Huang, Xuewei Zhao, Shijie Ke, You‐Yi Chen, Wan-Lin Wu, Jui‐Ling Hsu, Yu-Fu Lin, Ming‐Der Huang, Chia‐Ying Li, Laiqiang Huang, Zhiwen Wang, Xiang Zhao, Wen-Ying Zhong, Donghui Peng, Sagheer Ahmad, Siren Lan, Jisen Zhang, Wen‐Chieh Tsai, Yves Van de Peer, Zhong‐Jian Liu
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.