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

作　　者：Yanlei Feng Yukang Wang Hejun Lu Jun Li Delara Akhter Fang Liu Ting Zhao Xingxing Shen Xiaobo Li James Whelan Tianzhen Zhang Jianping Hu Ronghui Pan 

机构地区：[1]College of Agriculture and Biotechnology&ZJU-Hangzhou Global Scientific and Technological Innovation Center,Zhejiang University,Hangzhou 310058/311215,Zhejiang,China [2]Zhejiang Laboratory,Hangzhou 311121,Zhejiang,China [3]Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province,School of Life Sciences,Westlake University,Hangzhou 310024,Zhejiang,China [4]Department of Genetics and Plant Breeding,Sylhet Agricultural University,Sylhet 3100,Bangladesh [5]State Key Laboratory of Cotton Biology,Institute of Cotton Research,Chinese Academy of Agricultural Sciences,Anyang 450000,Henan,China [6]Institute of Biology,Westlake Institute for Advanced Study,Hangzhou 310024,Zhejiang,China [7]College of Life Science,Zhejiang University,Hangzhou 310058,Zhejiang,China [8]Michigan State University,Department of Energy Plant Research Laboratory and Plant Biology Department,East Lansing,MI 48824,USA

出　　处：《The Crop Journal》2023年第6期1782-1792,共11页作物学报（英文版）

基　　金：the Zhejiang Natural Science Foundation Outstanding Youth Grant(LR20C020002);the Zhejiang Provincial Natural Science Foundation of China(LZ23C020002);the National Natural Science Foundation of China(32200231);the National Key Research and Development Program of China(2022YFD1401600);the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2019R01002);Key Research Project of Zhejiang Lab(2021PE0AC04);the U.S.National Science Foundation(MCB 2148206).

摘　　要：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.

关 键 词：Cotton evolution Cotton phylogeny Lint fiber cotton Mitochondrial genome Mitochondrial genes 

分 类 号：S637[农业科学—蔬菜学]