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Research paper | Open Access

Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution

Yanlei Fenga,b,c,1, Yukang Wanga,b,1, Hejun Lua,1, Jun Lia, Delara Akhtera,b,d, Fang Liue, Ting Zhaoa, Xingxing Shena, Xiaobo Lic,f, James Whelang, Tianzhen Zhanga, Jianping Huh, Ronghui Pana,b( )
College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058/311215, Zhejiang, China
Zhejiang Laboratory, Hangzhou 311121, Zhejiang, China
Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet 3100, Bangladesh
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 450000, Henan, China
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
College of Life Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
Michigan State University, Department of Energy Plant Research Laboratory and Plant Biology Department, East Lansing, MI 48824, USA

1 These authors contributed equally to this work.

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Abstract

Cotton is a major crop that provides the most important renewable textile fibers in the world. Studies of the taxonomy and evolution of cotton species have received wide attentions, not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin, evolution, and cultivation of polyploid species. Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation. Whereas, with only a few mitogenomes assembled in the cotton genus Gossypium, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A–G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. Finally, these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

Keywords

Mitochondrial genomeCotton evolutionCotton phylogenyLint fiber cottonMitochondrial genes

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The Crop Journal
Volume 11 Issue 6,
December 2023
Pages 1782-1792
DOI: 10.1016/j.cj.2023.05.004
Cite this article:
Feng Y, Wang Y, Lu H, et al. Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution. The Crop Journal, 2023, 11(6): 1782-1792. https://doi.org/10.1016/j.cj.2023.05.004

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Received: 13 April 2023
Revised: 11 May 2023
Accepted: 15 June 2023
Published: 29 June 2023
© 2023 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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