ArticleNature biotechnology2015
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
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Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 923 papers.
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923citing papers in PubMed
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923 citing papers in PubMed.
- Genomic characterization of a MAGIC population containing introgressions from four tetraploid Gossypium species.The plant genome · 2026Article
- Engineering cotton with ASAL and MYB genes confer dual benefits of pest resistance and fiber improvement.Planta · 2026Article
- Day-neutral flowering candidate genes identified by selection mapping in an upland cotton (Gossypium hirsutum L.) RIL population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Integration of NIRS and GWAS identifies GhMYB86 as a potential regulator of cottonseed protein content with pleiotropic effects on fiber strength in upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
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- Phased T2T genome of a tetraploid grapevine reveals segmental allopolyploid origin and allele-specific alternative splicing during fruit development.Plant physiology · 2026Article
- Distinct evolutionary trajectories of gene duplication modes in 40 diploid cotton genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Comprehensive analysis of cotton AMT genes and functional analysis of the GhAMT1.4a in nitrogen metabolism.Functional & integrative genomics · 2026Article
- Genomic and population analyses reveal asymmetric subgenome evolution and local adaptation in the polyploid Lycopus lucidus.Communications biology · 2026Article
- Functional Analysis ofPlants (Basel, Switzerland) · 2026Article
- Whole-genome sequencing revealed the genomic origin of Solanum demissum Lindl., a Mexican hexaploid wild potato species.BMC plant biology · 2026Article
- Harnessing GhGRDP1 natural variation for enhanced cotton seed yield: a rhamnose-dependent strategy in breeding.Journal of advanced research · 2026Article
- A genome-wide association study to elucidate the genetic basis of the cottonseed protein content in Upland cotton (Breeding science · 2026Article
- A pangenome reference and population studies link structural variants with breeding traits in Gossypium hirsutum.Nature genetics · 2026Article
- Article
- Fine mapping and functional analysis of the candidate gene OFP17, regulating both seed and fruit sizes in cotton.The plant genome · 2026Article
- GhGLDH35A gene-mediated ROS homeostasis and stomatal movement via the ascorbic acid pathway confers alkaline stress tolerance.Journal of advanced research · 2026Article
- Expression genome-wide association analysis (eGWAS) identifies a candidate gene influencing fatty acid composition in soybeans.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Remodeling of homoeolog expression bias buffers stress response in allotetraploid cotton.BMC plant biology · 2026Article
- Structural Variation and 3D Genome-Driven DNA/RNA Methylation Divergence Contributing to Cotton Fiber Domestication.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
863 more citing papers are in PubMed but not listed here.
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Authors and funding
54 authors.
Tianzhen ZhangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Yan HuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Wenkai JiangNovogene Bioinformatics Institute, Beijing, China.
Lei Fang1] 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.
Xueying Guan1] 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.
Jiedan ChenState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.ORCID 0000000252238243
Jinbo ZhangNovogene Bioinformatics Institute, Beijing, China.
Christopher A SaskiClemson University Genomics Institute, Clemson University, Clemson, South Carolina, USA.
Brian E SchefflerUS Department of Agriculture (USDA), Agricultural Research Service (ARS), Middle Southern Area (MSA) Genomics Laboratory, Stoneville, Mississippi, USA.
David M StellyDepartment of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
Amanda M Hulse-KempDepartment of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
Qun WanState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Bingliang LiuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Chunxiao LiuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Sen WangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Mengqiao PanState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Yangkun WangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Dawei WangNovogene Bioinformatics Institute, Beijing, China.
Wenxue YeState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Lijing ChangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Wenpan ZhangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Qingxin SongDepartment 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.
Ryan C KirkbrideDepartment 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.
Xiaoya ChenNational 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.
Elizabeth DennisThe Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, Australia.
Danny J LlewellynThe Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, Australia.
Daniel G PetersonDepartment of Plant and Soil Sciences, Mississippi State University, Starkville, Mississippi, USA.
Peggy ThaxtonDelta Research and Extension Center, Mississippi State University, Stoneville, Mississippi, USA.
Don C JonesCotton Incorporated, Cary, North Carolina, USA.
Qiong WangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Xiaoyang XuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Hua ZhangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Huaitong WuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Lei ZhouState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Gaofu MeiState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Shuqi ChenState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Yue TianState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Dan XiangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Xinghe LiState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Jian DingState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Qiyang ZuoNovogene Bioinformatics Institute, Beijing, China.
Linna TaoNovogene Bioinformatics Institute, Beijing, China.
Yunchao LiuNovogene Bioinformatics Institute, Beijing, China.
Ji LiNovogene Bioinformatics Institute, Beijing, China.
Yu LinNovogene Bioinformatics Institute, Beijing, China.
Yuanyuan HuiNovogene Bioinformatics Institute, Beijing, China.
Zhisheng CaoNovogene Bioinformatics Institute, Beijing, China.
Caiping CaiState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Xiefei ZhuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Zhi JiangNovogene Bioinformatics Institute, Beijing, China.
Baoliang ZhouState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Wangzhen GuoState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, China.
Ruiqiang LiNovogene Bioinformatics Institute, Beijing, China.
Z Jeffrey Chen1] 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.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Cotton FiberGenome, PlantBase SequenceChromosome MappingGossypiumHigh-Throughput Nucleotide SequencingPlant ProteinsSequence Analysis, DNATetraploidyPlant Proteins
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