Article

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

Daojun YuanNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaZhonghui TangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaMaojun WangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaWenhui GaoNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaLili TuNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaXin JinNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaLing‐Ling ChenCollege of Informatics, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaYonghui HeNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaLin ZhangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaLongfu ZhuNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaLi YangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaQiqi LiangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaZhongxu LinNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaXiyan YangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaNian LiuNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaShuangxia JinNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaLei YangCollege of Informatics, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaYuanhao DingNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaGuoliang LiCollege of Informatics, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaXiaoan RuanNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, ChinaYijun RuanDepartment of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Ave, Farmington, CT 06032, USAXianlong ZhangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Wuhan, Hubei 430070, China

2015en

ABI

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.

Identifiers

DOI: 10.1038/srep17662

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