Genome sequence of the cultivated cotton Gossypium arboreum.
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.
1] State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. [2].
Fuguang
F
Li
1] BGI-Shenzhen, Shenzhen, China. [2].
Guangyi
G
Fan
1] State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. [2].
Kunbo
K
Wang
1] BGI-Shenzhen, Shenzhen, China. [2].
Fengming
F
Sun
1] State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. [2].
Youlu
Y
Yuan
1] State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. [2].
Guoli
G
Song
1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2].
Qin
Q
Li
1] Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China. [2].
Zhiying
Z
Ma
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Cairui
C
Lu
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Changsong
C
Zou
BGI-Shenzhen, Shenzhen, China.
Wenbin
W
Chen
BGI-Shenzhen, Shenzhen, China.
Xinming
X
Liang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Haihong
H
Shang
BGI-Shenzhen, Shenzhen, China.
Weiqing
W
Liu
BGI-Shenzhen, Shenzhen, China.
Chengcheng
C
Shi
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
Guanghui
G
Xiao
BGI-Shenzhen, Shenzhen, China.
Caiyun
C
Gou
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Wuwei
W
Ye
BGI-Shenzhen, Shenzhen, China.
Xun
X
Xu
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Xueyan
X
Zhang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Hengling
H
Wei
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Zhifang
Z
Li
Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China.
Guiyin
G
Zhang
BGI-Shenzhen, Shenzhen, China.
Junyi
J
Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Kun
K
Liu
Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
Russell J
RJ
Kohel
Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
Richard G
RG
Percy
Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
John Z
JZ
Yu
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
Yu-Xian
YX
Zhu
1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] King Abdulaziz University, Jeddah, Saudi Arabia. [4] Macau University of Science and Technology, Macau, China. [5] Department of Medicine, University of Hong Kong, Hong Kong. [6] State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong.
Jun
J
Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
Shuxun
S
Yu
D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods; D018744:DNA, Plant; D060467:Disease Resistance / Q000235:genetics; D005030:Ethylenes / Q000737:chemistry; D019143:Evolution, Molecular; D015723:Gene Library; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000517:prevention & control; D011123:Polyploidy; D018626:Retroelements; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D020079:Terminal Repeat Sequences; D059467:Transcriptome; D020172:Verticillium
D018744:DNA, Plant; D005030:Ethylenes; D018626:Retroelements; C036216:ethylene