title: Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
abstract: Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Fuguang
authors.initials: F
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Cairui
authors.initials: C
authors.lastname: Lu
authors.affiliation: 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China.
authors.forename: Guanghui
authors.initials: G
authors.lastname: Xiao
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Changsong
authors.initials: C
authors.lastname: Zou
authors.affiliation: Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
authors.forename: Russell J
authors.initials: RJ
authors.lastname: Kohel
authors.affiliation: Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China.
authors.forename: Zhiying
authors.initials: Z
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Haihong
authors.initials: H
authors.lastname: Shang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Xiongfeng
authors.initials: X
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Jianyong
authors.initials: J
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xinming
authors.initials: X
authors.lastname: Liang
authors.affiliation: 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China.
authors.forename: Gai
authors.initials: G
authors.lastname: Huang
authors.affiliation: Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Percy
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Weihua
authors.initials: W
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Chen
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: BGI-Shenzhen, Shenzhen, China.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Youlu
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Wuwei
authors.initials: W
authors.lastname: Ye
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Xueyan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Weiqing
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Hengling
authors.initials: H
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Shoujun
authors.initials: S
authors.lastname: Wei
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Guodong
authors.initials: G
authors.lastname: Huang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Agronomy, Zhejiang University, Hangzhou, China.
authors.forename: Shuijin
authors.initials: S
authors.lastname: Zhu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: He
authors.initials: H
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Fengming
authors.initials: F
authors.lastname: Sun
authors.affiliation: Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China.
authors.forename: Xingfen
authors.initials: X
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jiahao
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: He
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Leihuan
authors.initials: L
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Jinjie
authors.initials: J
authors.lastname: Cui
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Guoli
authors.initials: G
authors.lastname: Song
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Kunbo
authors.initials: K
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
authors.forename: John Z
authors.initials: JZ
authors.lastname: Yu
authors.affiliation: 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China.
authors.forename: Yuxian
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Shuxun
authors.initials: S
authors.lastname: Yu
mesh_terms: D000594:Amino Acid Oxidoreductases / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D032561:Cotton Fiber; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant; D005964:Glucosyltransferases / Q000235:genetics; D003368:Gossypium / Q000235:genetics*; D010802:Phylogeny; D011123:Polyploidy; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D000594:Amino Acid Oxidoreductases; C059460:1-aminocyclopropane-1-carboxylic acid oxidase; D005964:Glucosyltransferases; C478648:cellulose synthase