Format

Send to

Choose Destination
Nat Biotechnol. 2015 May;33(5):531-7. doi: 10.1038/nbt.3207. Epub 2015 Apr 20.

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

Author information

1
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
2
Novogene Bioinformatics Institute, Beijing, China.
3
1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China. [2] Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
4
Clemson University Genomics Institute, Clemson University, Clemson, South Carolina, USA.
5
US Department of Agriculture (USDA), Agricultural Research Service (ARS), Middle Southern Area (MSA) Genomics Laboratory, Stoneville, Mississippi, USA.
6
Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
7
Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
8
National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
9
The Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, Australia.
10
Department of Plant and Soil Sciences, Mississippi State University, Starkville, Mississippi, USA.
11
Delta Research and Extension Center, Mississippi State University, Stoneville, Mississippi, USA.
12
Cotton Incorporated, Cary, North Carolina, USA.

Abstract

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.

PMID:
25893781
DOI:
10.1038/nbt.3207
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center