Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
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, ChinaYan HuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaWenkai JiangNovogene Bioinformatics Institute, Beijing, ChinaLei 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, USAXueying 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, USAJiedan ChenState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaJinbo ZhangNovogene Bioinformatics Institute, Beijing, ChinaChristopher SaskiClemson University Genomics Institute, Clemson University, Clemson, South Carolina, USABrian E. SchefflerUS Department of Agriculture (USDA), Agricultural Research Service (ARS), Middle Southern Area (MSA) Genomics Laboratory, Stoneville, Mississippi, USADavid M. StellyDepartment of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USAAmanda M. Hulse‐KempDepartment of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USAQun WanState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaBingliang LiuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaChunxiao LiuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaSen WangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaMengqiao PanState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaYangkun WangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaDawei WangNovogene Bioinformatics Institute, Beijing, ChinaWenxue YeState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaLijing ChangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaWenpan ZhangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaQingxin 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, USARyan 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, USAXiao‐Ya 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, ChinaElizabeth S. DennisThe Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, AustraliaDanny LlewellynThe Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Black Mountain, AustraliaDaniel G. PetersonDepartment of Plant and Soil Sciences, Mississippi State University, Starkville, Mississippi, USAP. M. ThaxtonDelta Research and Extension Center, Mississippi State University, Stoneville, Mississippi, USADon C. JonesCotton Incorporated, Cary, North Carolina, USAQiong WangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaXiaoyang XuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaHua ZhangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaHuaitong WuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaLei ZhouState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaGaofu MeiState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaShuqi ChenState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaYue TianState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaDan XiangState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaXinghe LiState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaJian DingState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaQiyang ZuoNovogene Bioinformatics Institute, Beijing, ChinaLinna TaoNovogene Bioinformatics Institute, Beijing, ChinaYunchao LiuNovogene Bioinformatics Institute, Beijing, ChinaJi LiNovogene Bioinformatics Institute, Beijing, ChinaYu LinNovogene Bioinformatics Institute, Beijing, ChinaYuanyuan HuiNovogene Bioinformatics Institute, Beijing, ChinaZhisheng CaoNovogene Bioinformatics Institute, Beijing, ChinaCaiping CaiState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaXiefei ZhuState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaZhi JiangNovogene Bioinformatics Institute, Beijing, ChinaBaoliang ZhouState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaWangzhen GuoState Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Jiangsu, ChinaRuiqiang LiNovogene Bioinformatics Institute, Beijing, ChinaZ. 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
2015en
ABI
Annotatsiya
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.
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