Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
Tianzhen Zhang, Yan Hu, Wenkai Jiang, Lei Fang, Xueying Guan, Jiedan Chen, Jinbo Zhang, Christopher Saski, Brian E. Scheffler, David M. Stelly, Amanda M. Hulse‐Kemp, Qun Wan, Bingliang Liu, Chunxiao Liu, Sen Wang, Mengqiao Pan, Yangkun Wang, Dawei Wang, Wenxue Ye, Lijing Chang, Wenpan Zhang, Qingxin Song, Ryan C. Kirkbride, Xiao‐Ya Chen, Elizabeth S. Dennis, Danny Llewellyn, Daniel G. Peterson, P. M. Thaxton, Don C. Jones, Qiong Wang, Xiaoyang Xu, Hua Zhang, Huaitong Wu, Lei Zhou, Gaofu Mei, Shuqi Chen, Yue Tian, Dan Xiang, Xinghe Li, Jian Ding, Qiyang Zuo, Linna Tao, Yunchao Liu, Ji Li, Yu Lin, Yuanyuan Hui, Zhisheng Cao, Caiping Cai, Xiefei Zhu, Zhi Jiang, Baoliang Zhou, Wangzhen Guo, Ruiqiang Li, Z. Jeffrey Chen
Abstract
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.