Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

• Published in: Nature biotechnology Vol. 33; no. 5; pp. 531 - 537
• Main Authors: Zhang, Tianzhen, Hu, Yan, Jiang, Wenkai, Fang, Lei, Guan, Xueying, Chen, Jiedan, Zhang, Jinbo, Saski, Christopher A, Scheffler, Brian E, Stelly, David M, Hulse-Kemp, Amanda M, Wan, Qun, Liu, Bingliang, Liu, Chunxiao, Wang, Sen, Pan, Mengqiao, Wang, Yangkun, Wang, Dawei, Ye, Wenxue, Chang, Lijing, Zhang, Wenpan, Song, Qingxin, Kirkbride, Ryan C, Chen, Xiaoya, Dennis, Elizabeth, Llewellyn, Danny J, Peterson, Daniel G, Thaxton, Peggy, Jones, Don C, Wang, Qiong, Xu, Xiaoyang, Zhang, Hua, Wu, Huaitong, Zhou, Lei, Mei, Gaofu, Chen, Shuqi, Tian, Yue, Xiang, Dan, Li, Xinghe, Ding, Jian, Zuo, Qiyang, Tao, Linna, Liu, Yunchao, Li, Ji, Lin, Yu, Hui, Yuanyuan, Cao, Zhisheng, Cai, Caiping, Zhu, Xiefei, Jiang, Zhi, Zhou, Baoliang, Guo, Wangzhen, Li, Ruiqiang, Chen, Z Jeffrey
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2015; Nature Publishing Group
• Subjects: 38/39; 38/91; 45/23; 631/208/212/2304; 631/208/2491/3933; 631/449/711; 631/61/514/2254; Agriculture; Base Sequence; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Chromosome Mapping; Cotton; Cotton Fiber; Crops; DNA sequencing; Domestication; Genome, Plant; Genomes; Gossypium - genetics; Gossypium hirsutum; High-Throughput Nucleotide Sequencing; Identification and classification; Life Sciences; Methods; Nucleotide sequencing; Plant Proteins - biosynthesis; Plant Proteins - genetics; Polyploidy; Sequence Analysis, DNA; Tetraploidy
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/nbt.3207

Two draft sequences of Gossypium hirsutum, the most widely cultivated cotton species, provide insights into genome structure, genome rearrangement, gene evolution and cotton fiber biology. Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.