Genome sequence of the cultivated cotton Gossypium arboreum

Yu-Xian Zhu, Jun Wang, Shuxun Yu and colleagues report sequencing and assembly of the genome of cultivated cotton, Gossypium arboreum . Comparison with the Gossypium raimondii genome sequence provides insights into genome evolution and speciation, and identifies two shared whole-genome duplication events occurring before the speciation event around 2–13 million years ago. The complex allotetraploid nature of the cotton genome (AADD; 2 n = 52) makes genetic, genomic and functional analyses extremely challenging. Here we sequenced and assembled the Gossypium arboreum (AA; 2 n = 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.