1. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
- Author
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Amanda M. Hulse-Kemp, Dan Xiang, Tianzhen Zhang, Lei Fang, Xiaoyang Xu, Ryan C. Kirkbride, Don C. Jones, Xinghe Li, Qiyang Zuo, Yan Hu, Ji Li, Yuanyuan Hui, Mengqiao Pan, Jiedan Chen, Bingliang Liu, Qun Wan, Christopher A. Saski, Sen Wang, Huaitong Wu, Linna Tao, Xiao-Ya Chen, Yangkun Wang, Qingxin Song, Shuqi Chen, Zhisheng Cao, Dawei Wang, Lijing Chang, Yue Tian, Xueying Guan, Hua Zhang, Z. Jeffrey Chen, Jian Ding, Wenkai Jiang, Yunchao Liu, Lei Zhou, Gaofu Mei, Qiong Wang, Chunxiao Liu, David M. Stelly, Xiefei Zhu, Yu Lin, Danny J. Llewellyn, Ruiqiang Li, Zhi Jiang, Daniel G. Peterson, Elizabeth S. Dennis, Wenpan Zhang, Wangzhen Guo, Peggy Thaxton, Caiping Cai, Baoliang Zhou, Brian E. Scheffler, Wenxue Ye, and Jinbo Zhang
- Subjects
Sequence analysis ,Biomedical Engineering ,Bioengineering ,Biology ,Gossypium raimondii ,Applied Microbiology and Biotechnology ,Genome ,Polyploid ,Cotton Fiber ,Domestication ,Gene ,Plant Proteins ,Genetics ,Whole genome sequencing ,Bacterial artificial chromosome ,Gossypium ,Base Sequence ,food and beverages ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Tetraploidy ,Molecular Medicine ,Genome, Plant ,Biotechnology - Abstract
© 2015 Nature America, Inc. All rights reserved. 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.
- Published
- 2014