title: The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres.
abstract: Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853 Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade, and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a "relay race"-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Daojun
authors.initials: D
authors.lastname: Yuan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.|The Jackson Laboratory for Genome Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
authors.forename: Zhonghui
authors.initials: Z
authors.lastname: Tang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Maojun
authors.initials: M
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Wenhui
authors.initials: W
authors.lastname: Gao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Tu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Jin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.|College of Informatics, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Chen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: He
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Longfu
authors.initials: L
authors.lastname: Zhu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Qiqi
authors.initials: Q
authors.lastname: Liang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Zhongxu
authors.initials: Z
authors.lastname: Lin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Xiyan
authors.initials: X
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Nian
authors.initials: N
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Shuangxia
authors.initials: S
authors.lastname: Jin
authors.affiliation: College of Informatics, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Lei
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Yuanhao
authors.initials: Y
authors.lastname: Ding
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.|The Jackson Laboratory for Genome Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.|College of Informatics, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Guoliang
authors.initials: G
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.|The Jackson Laboratory for Genome Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.|The Jackson Laboratory for Genome Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.|Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Ave, Farmington, CT 06032, USA.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D032561:Cotton Fiber; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011123:Polyploidy