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

Daojun Yuan,Guoliang Li,Nian Liu,Yang Lei,Lili Tu,Xiaoan Ruan,Maojun Wang,Xianlong Zhang,Yonghui He,Xiyan Yang,Xin Jin,Lingling Chen,Qiqi Liang,Yang Li,Yuanhao Ding,Yijun Ruan,Lin Zhang,Zhonghui Tang,Wenhui Gao,Shuangxia Jin,Longfu Zhu,Zhenhua Lin

doi:10.1038/srep17662

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.

Highlights

Cotton has been cultivated for its fibre for more than 7,000 years
To understand how allopolyploidization has led to desirable agronomic traits, it is necessary to uncover the sequences of the complete tetraploid cotton genome and to identify the specific genes involved in its superior fibre development
The complexity of allopolyploid crops has represented a challenge for the genomics community due to the co-residence of closely related homoeologous subgenomes; the study of many important crops including cotton has been hindered

Summary

Introduction

Cotton has been cultivated for its fibre for more than 7,000 years. Despite the availability of the petroleum-derived synthetic fibre alternatives, cotton fibre continues to serve as the world’s most important natural renewable sources for textiles. Arboreum9) and tetraploid G. hirsutum[10,11] have provided valuable reference genomes for cotton and a number of shotgun sequencing[12] efforts have increased our understanding of variations in the cotton genomes, our understanding of the impact of allopolyploidization on fibre production and quality at the genomic level remains minimal. To understand how allopolyploidization has led to desirable agronomic traits, it is necessary to uncover the sequences of the complete tetraploid cotton genome and to identify the specific genes involved in its superior fibre development. We report the genome sequence of the superior fibre quality tetraploid cotton, G. barbadense acc. The G. barbadense genome sequence and our analyses presented in this study provide a new set of valuable resources, which can be of great importance to identify candidate genes and to study their interplay for improving the cotton fibre quality and productivity. We believe that the characterization of the tetraploid G. barbadense genome represents a major advance in our understanding of the dynamics of the cotton genome, and provides novel insights into the mechanism of polyploidization in plants

Methods

Results

Conclusion