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Diploid and tetraploid genomes of Acorus and the evolution of monocots

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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. Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.
Keywords
General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary, MULTIPLE SEQUENCE ALIGNMENT, CUP-SHAPED-COTYLEDON, MAXIMUM-LIKELIHOOD, ANCIENT POLYPLOIDY, CENTRAL CELL, GENE, ARABIDOPSIS, DIVERGENCE, SECONDARY, PROTEIN

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MLA
Ma, Liang, et al. “Diploid and Tetraploid Genomes of Acorus and the Evolution of Monocots.” NATURE COMMUNICATIONS, vol. 14, no. 1, 2023, doi:10.1038/s41467-023-38829-3.
APA
Ma, L., Liu, K.-W., Li, Z., Hsiao, Y.-Y., Qi, Y., Fu, T., … Liu, Z.-J. (2023). Diploid and tetraploid genomes of Acorus and the evolution of monocots. NATURE COMMUNICATIONS, 14(1). https://doi.org/10.1038/s41467-023-38829-3
Chicago author-date
Ma, Liang, Ke-Wei Liu, Zhen Li, Yu-Yun Hsiao, Yiying Qi, Tao Fu, Guang-Da Tang, et al. 2023. “Diploid and Tetraploid Genomes of Acorus and the Evolution of Monocots.” NATURE COMMUNICATIONS 14 (1). https://doi.org/10.1038/s41467-023-38829-3.
Chicago author-date (all authors)
Ma, Liang, 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 Van de Peer, and Zhong-Jian Liu. 2023. “Diploid and Tetraploid Genomes of Acorus and the Evolution of Monocots.” NATURE COMMUNICATIONS 14 (1). doi:10.1038/s41467-023-38829-3.
Vancouver
1.
Ma L, Liu K-W, Li Z, Hsiao Y-Y, Qi Y, Fu T, et al. Diploid and tetraploid genomes of Acorus and the evolution of monocots. NATURE COMMUNICATIONS. 2023;14(1).
IEEE
[1]
L. Ma et al., “Diploid and tetraploid genomes of Acorus and the evolution of monocots,” NATURE COMMUNICATIONS, vol. 14, no. 1, 2023.
@article{01H43N8DSC08TVH3K7G72JB0BH,
  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. Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.}},
  articleno    = {{3661}},
  author       = {{Ma, Liang and Liu, Ke-Wei and Li, Zhen and Hsiao, Yu-Yun and Qi, Yiying and Fu, Tao and Tang, Guang-Da and Zhang, Diyang and Sun, Wei-Hong and Liu, Ding-Kun and Li, Yuanyuan and Chen, Gui-Zhen and Liu, Xue-Die and Liao, Xing-Yu and Jiang, Yu-Ting and Yu, Xia and Hao, Yang and Huang, Jie and Zhao, Xue-Wei and Ke, Shijie and Chen, You-Yi and Wu, Wan-Lin and Hsu, Jui-Ling and Lin, Yu-Fu and Huang, Ming-Der and Li, Chia-Ying and Huang, Laiqiang and Wang, Zhi-Wen and Zhao, Xiang and Zhong, Wen-Ying and Peng, Dong-Hui and Ahmad, Sagheer and Lan, Siren and Zhang, Ji-Sen and Tsai, Wen-Chieh and Van de Peer, Yves and Liu, Zhong-Jian}},
  issn         = {{2041-1723}},
  journal      = {{NATURE COMMUNICATIONS}},
  keywords     = {{General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary,MULTIPLE SEQUENCE ALIGNMENT,CUP-SHAPED-COTYLEDON,MAXIMUM-LIKELIHOOD,ANCIENT POLYPLOIDY,CENTRAL CELL,GENE,ARABIDOPSIS,DIVERGENCE,SECONDARY,PROTEIN}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{18}},
  title        = {{Diploid and tetraploid genomes of Acorus and the evolution of monocots}},
  url          = {{http://doi.org/10.1038/s41467-023-38829-3}},
  volume       = {{14}},
  year         = {{2023}},
}

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