title: Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons.
abstract: Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.
  
  
  
  We resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species. Phylogenetic analysis shows two divergent groups for G. hirsutum and G. barbadense, suggesting a dual domestication processes in tetraploid cottons. In spite of the strong genetic divergence, a small number of interspecific reciprocal introgression events are found between these species and the introgression pattern is significantly biased towards the gene flow from G. hirsutum into G. barbadense. We identify selective sweeps, some of which are associated with relatively highly expressed genes for fiber development and seed germination.
  
  
  
  We report a comprehensive analysis of the evolution and domestication history of allotetraploid cottons based on the whole genomic variation between G. hirsutum and G. barbadense and between wild accessions and modern cultivars. These results provide genomic bases for improving cotton production and for further evolution analysis of polyploid crops.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Fang
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Chunxiao
authors.initials: C
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Baoliang
authors.initials: B
authors.lastname: Zhou
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Yangkun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Shuqi
authors.initials: S
authors.lastname: Chen
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA.
authors.forename: David D
authors.initials: DD
authors.lastname: Fang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Xiongming
authors.initials: X
authors.lastname: Du
authors.affiliation: Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Sciences, Xinjiang, 832000, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Jiedan
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Sen
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Wan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Bingliang
authors.initials: B
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Mengqiao
authors.initials: M
authors.lastname: Pan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Lijing
authors.initials: L
authors.lastname: Chang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Huaitong
authors.initials: H
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Gaofu
authors.initials: G
authors.lastname: Mei
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Xiang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Xinghe
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Caiping
authors.initials: C
authors.lastname: Cai
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Xiefei
authors.initials: X
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.|Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, the University of Texas at Austin, Austin, TX, 78712, USA.
authors.forename: Z Jeffrey
authors.initials: ZJ
authors.lastname: Chen
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.affiliation: State Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Xiaoya
authors.initials: X
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wangzhen
authors.initials: W
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China. cotton@njau.edu.cn.|Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310029, China. cotton@njau.edu.cn.
authors.forename: Tianzhen
authors.initials: T
authors.lastname: Zhang
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China. xhhuang@shnu.edu.cn.|College of life and environmental sciences, Shanghai Normal University, Shanghai, 200234, China. xhhuang@shnu.edu.cn.
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
mesh_terms: D000220:Adaptation, Biological; D032461:Chromosomes, Plant; D000071278:Domestication; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005838:Genotype; D003368:Gossypium / Q000145:classification / Q000235:genetics*; D054643:INDEL Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic; D057891:Tetraploidy
keywords: Allotetraploid cottons; Divergence; Domestication; Resequencing