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Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

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Abstract
Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)(6), Ge] and Gossypium stephensii [(AD)(7), Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)(1), Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergenc-ethat contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/ absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA delta isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.
Keywords
Multidisciplinary, tetraploid cotton, polyploid dynamics, structure variations, adaptive evolution

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Citation

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MLA
Peng, Renhai, et al. “Evolutionary Divergence of Duplicated Genomes in Newly Described Allotetraploid Cottons.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 119, no. 39, 2022, doi:10.1073/pnas.2208496119.
APA
Peng, R., Xu, Y., Tian, S., Unver, T., Liu, Z., Zhou, Z., … Liu, F. (2022). Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(39). https://doi.org/10.1073/pnas.2208496119
Chicago author-date
Peng, Renhai, Yanchao Xu, Shilin Tian, Turgay Unver, Zhen Liu, Zhongli Zhou, Xiaoyan Cai, et al. 2022. “Evolutionary Divergence of Duplicated Genomes in Newly Described Allotetraploid Cottons.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 119 (39). https://doi.org/10.1073/pnas.2208496119.
Chicago author-date (all authors)
Peng, Renhai, Yanchao Xu, Shilin Tian, Turgay Unver, Zhen Liu, Zhongli Zhou, Xiaoyan Cai, Kunbo Wang, Yangyang Wei, Yuling Liu, Heng Wang, Guanjing Hu, Zhongren Zhang, Corrinne E. Grover, Yuqing Hou, Yuhong Wang, Pengtao Li, Tao Wang, Quanwei Lu, Yuanyuan Wang, Justin L. Conover, Hassan Ghazal, Qinglian Wang, Baohong Zhang, Marc Van Montagu, Yves Van de Peer, Jonathan F. Wendel, and Fang Liu. 2022. “Evolutionary Divergence of Duplicated Genomes in Newly Described Allotetraploid Cottons.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 119 (39). doi:10.1073/pnas.2208496119.
Vancouver
1.
Peng R, Xu Y, Tian S, Unver T, Liu Z, Zhou Z, et al. Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2022;119(39).
IEEE
[1]
R. Peng et al., “Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons,” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 119, no. 39, 2022.
@article{8768840,
  abstract     = {{Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)(6), Ge] and Gossypium stephensii [(AD)(7), Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)(1), Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergenc-ethat contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/ absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA delta isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.
}},
  articleno    = {{e2208496119}},
  author       = {{Peng, Renhai and Xu, Yanchao and Tian, Shilin and Unver, Turgay and Liu, Zhen and Zhou, Zhongli and Cai, Xiaoyan and Wang, Kunbo and Wei, Yangyang and Liu, Yuling and Wang, Heng and Hu, Guanjing and Zhang, Zhongren and Grover, Corrinne E. and Hou, Yuqing and Wang, Yuhong and Li, Pengtao and Wang, Tao and Lu, Quanwei and Wang, Yuanyuan and Conover, Justin L. and Ghazal, Hassan and Wang, Qinglian and Zhang, Baohong and Van Montagu, Marc and Van de Peer, Yves and Wendel, Jonathan F. and Liu, Fang}},
  issn         = {{0027-8424}},
  journal      = {{PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}},
  keywords     = {{Multidisciplinary,tetraploid cotton,polyploid dynamics,structure variations,adaptive evolution}},
  language     = {{eng}},
  number       = {{39}},
  pages        = {{11}},
  title        = {{Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons}},
  url          = {{http://doi.org/10.1073/pnas.2208496119}},
  volume       = {{119}},
  year         = {{2022}},
}

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