Genome sequence of the cultivated cotton Gossypium arboreum

Fuguang Li, Guangyi Fan, Kunbo Wang, Fengming Sun, Youlu Yuan, Guoli Song, Qin Li, Zhiying Ma, Cairui Lu, Changsong Zou, Wenbin Chen, Xinming Liang, Haihong Shang, Weiqing Liu, Chengcheng Shi, Guanghui Xiao, Caiyun Gou, Wuwei Ye, Xun Xu, Xueyan Zhang, Hengling Wei, Zhifang Li, Guiyin Zhang, Junyi Wang, Kun Liu, Russell J Kohel, Richard G Percy, John Z Yu, Yu-Xian Zhu, Jun Wang, Shuxun Yu
Nature Genetics 2014, 46 (6): 567-72
The complex allotetraploid nature of the cotton genome (AADD; 2n = 52) makes genetic, genomic and functional analyses extremely challenging. Here we sequenced and assembled the Gossypium arboreum (AA; 2n = 26) genome, a putative contributor of the A subgenome. A total of 193.6 Gb of clean sequence covering the genome by 112.6-fold was obtained by paired-end sequencing. We further anchored and oriented 90.4% of the assembly on 13 pseudochromosomes and found that 68.5% of the genome is occupied by repetitive DNA sequences. We predicted 41,330 protein-coding genes in G. arboreum. Two whole-genome duplications were shared by G. arboreum and Gossypium raimondii before speciation. Insertions of long terminal repeats in the past 5 million years are responsible for the twofold difference in the sizes of these genomes. Comparative transcriptome studies showed the key role of the nucleotide binding site (NBS)-encoding gene family in resistance to Verticillium dahliae and the involvement of ethylene in the development of cotton fiber cells.

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