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Nat Biotechnol. 2015 May;33(5):524-30. doi: 10.1038/nbt.3208. Epub 2015 Apr 20.

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.

Author information

State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
BGI-Shenzhen, Shenzhen, China.
1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China.
Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA.
Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Department of Agronomy, Zhejiang University, Hangzhou, China.


Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.

[Indexed for MEDLINE]

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