title: Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.
abstract: Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11-20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.
authors.affiliation: Esquel Group, 25/F Eastern Cenrtal Plaza, 3 Yin Hing Road, Shau Kei Wan, Hongkong, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Liu
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 200032, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhao
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Hua-Jun
authors.initials: HJ
authors.lastname: Zheng
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Gang
authors.initials: G
authors.lastname: Lu
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 200032, China.
authors.forename: Chang-Qing
authors.initials: CQ
authors.lastname: Yang
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Jie-Dan
authors.initials: JD
authors.lastname: Chen
authors.affiliation: Esquel Group, 25/F Eastern Cenrtal Plaza, 3 Yin Hing Road, Shau Kei Wan, Hongkong, China.
authors.forename: Jun-Jian
authors.initials: JJ
authors.lastname: Chen
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 200032, China.
authors.forename: Dian-Yang
authors.initials: DY
authors.lastname: Chen
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.|State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
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 200032, China.
authors.forename: Ling-Jian
authors.initials: LJ
authors.lastname: Wang
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Wang-Zhen
authors.initials: WZ
authors.lastname: Guo
authors.affiliation: Esquel Group, 25/F Eastern Cenrtal Plaza, 3 Yin Hing Road, Shau Kei Wan, Hongkong, China.
authors.forename: Yu-Lin
authors.initials: YL
authors.lastname: Bai
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 200032, China.
authors.forename: Ju-Xin
authors.initials: JX
authors.lastname: Ruan
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 200032, China.
authors.forename: Xiao-Xia
authors.initials: XX
authors.lastname: Shangguan
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 200032, China.
authors.forename: Ying-Bo
authors.initials: YB
authors.lastname: Mao
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 200032, China.
authors.forename: Chun-Min
authors.initials: CM
authors.lastname: Shan
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Jian-Ping
authors.initials: JP
authors.lastname: Jiang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Yong-Qiang
authors.initials: YQ
authors.lastname: Zhu
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Jin
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Kang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Shu-Ting
authors.initials: ST
authors.lastname: Chen
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Xu-Lin
authors.initials: XL
authors.lastname: He
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Yue-Zhu
authors.initials: YZ
authors.lastname: Wang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Wang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Shu-Ting
authors.initials: ST
authors.lastname: Yu
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Bi-Yun
authors.initials: BY
authors.lastname: Wang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Wei
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Si-Chao
authors.initials: SC
authors.lastname: Song
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Xin-Yan
authors.initials: XY
authors.lastname: Lu
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Zheng-Chao
authors.initials: ZC
authors.lastname: Gao
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Wen-Yi
authors.initials: WY
authors.lastname: Gu
authors.affiliation: The Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu 214123, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Deng
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Ma
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Sen
authors.initials: S
authors.lastname: Wang
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Wen-Hua
authors.initials: WH
authors.lastname: Liang
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Fang
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Cai-Ping
authors.initials: CP
authors.lastname: Cai
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Xie-Fei
authors.initials: XF
authors.lastname: Zhu
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Bao-Liang
authors.initials: BL
authors.lastname: Zhou
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.|Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Jeffrey Chen
authors.affiliation: Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Shu-Hua
authors.initials: SH
authors.lastname: Xu
authors.affiliation: Esquel Group, 25/F Eastern Cenrtal Plaza, 3 Yin Hing Road, Shau Kei Wan, Hongkong, China.
authors.forename: Yu-Gao
authors.initials: YG
authors.lastname: Zhang
authors.affiliation: Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
authors.forename: Sheng-Yue
authors.initials: SY
authors.lastname: Wang
authors.affiliation: Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
authors.forename: Tian-Zhen
authors.initials: TZ
authors.lastname: Zhang
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 200032, China.|Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.|State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Guo-Ping
authors.initials: GP
authors.lastname: Zhao
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 200032, China.
authors.forename: Xiao-Ya
authors.initials: XY
authors.lastname: Chen
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D032461:Chromosomes, Plant; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D032561:Cotton Fiber; D020869:Gene Expression Profiling; D056726:Genetic Association Studies; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D003368:Gossypium / Q000235:genetics* / Q000378:metabolism*; D055432:Metabolomics / Q000379:methods; D058977:Molecular Sequence Annotation; D010641:Phenotype; D010802:Phylogeny; D011123:Polyploidy; D019655:Quantitative Trait, Heritable; D012717:Sesquiterpenes / Q000378:metabolism; D014178:Translocation, Genetic; D000094162:Phytoalexins
chemical_list: D012717:Sesquiterpenes; D019883:Alkyl and Aryl Transferases; C108877:terpene synthase; D000094162:Phytoalexins