title: Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
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, Jiangsu, China.
authors.forename: Tianzhen
authors.initials: T
authors.lastname: Zhang
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, Jiangsu, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Wenkai
authors.initials: W
authors.lastname: Jiang
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China. [2] Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Fang
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China. [2] Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
authors.forename: Xueying
authors.initials: X
authors.lastname: Guan
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, Jiangsu, China.
authors.forename: Jiedan
authors.identifier: 0000000252238243
authors.initials: J
authors.lastname: Chen
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Jinbo
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Clemson University Genomics Institute, Clemson University, Clemson, South Carolina, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Saski
authors.affiliation: US Department of Agriculture (USDA), Agricultural Research Service (ARS), Middle Southern Area (MSA) Genomics Laboratory, Stoneville, Mississippi, USA.
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Stelly
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
authors.forename: Amanda M
authors.initials: AM
authors.lastname: Hulse-Kemp
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, Jiangsu, 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, Jiangsu, 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, Jiangsu, 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, Jiangsu, 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, Jiangsu, 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, Jiangsu, China.
authors.forename: Yangkun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Dawei
authors.initials: D
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, Jiangsu, China.
authors.forename: Wenxue
authors.initials: W
authors.lastname: Ye
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, Jiangsu, 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, Jiangsu, China.
authors.forename: Wenpan
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
authors.forename: Qingxin
authors.initials: Q
authors.lastname: Song
authors.affiliation: Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
authors.forename: Ryan C
authors.initials: RC
authors.lastname: Kirkbride
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Xiaoya
authors.initials: X
authors.lastname: Chen
authors.affiliation: The Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, Australia.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Dennis
authors.affiliation: The Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, Australia.
authors.forename: Danny J
authors.initials: DJ
authors.lastname: Llewellyn
authors.affiliation: Department of Plant and Soil Sciences, Mississippi State University, Starkville, Mississippi, USA.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.affiliation: Delta Research and Extension Center, Mississippi State University, Stoneville, Mississippi, USA.
authors.forename: Peggy
authors.initials: P
authors.lastname: Thaxton
authors.affiliation: Cotton Incorporated, Cary, North Carolina, USA.
authors.forename: Don C
authors.initials: DC
authors.lastname: Jones
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, Jiangsu, 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, Jiangsu, China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Xu
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, Jiangsu, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Zhang
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, Jiangsu, 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, Jiangsu, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhou
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, Jiangsu, 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, Jiangsu, China.
authors.forename: Shuqi
authors.initials: S
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, Jiangsu, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Tian
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, Jiangsu, 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, Jiangsu, 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, Jiangsu, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ding
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Qiyang
authors.initials: Q
authors.lastname: Zuo
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Linna
authors.initials: L
authors.lastname: Tao
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Yunchao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Li
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Hui
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Zhisheng
authors.initials: Z
authors.lastname: Cao
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, Jiangsu, 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, Jiangsu, China.
authors.forename: Xiefei
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Jiang
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, Jiangsu, China.
authors.forename: Baoliang
authors.initials: B
authors.lastname: Zhou
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, Jiangsu, China.
authors.forename: Wangzhen
authors.initials: W
authors.lastname: Guo
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China. [2] Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
authors.forename: Z Jeffrey
authors.initials: ZJ
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032561:Cotton Fiber; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D017422:Sequence Analysis, DNA; D057891:Tetraploidy
chemical_list: D010940:Plant Proteins