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

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 all...

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Published inNature biotechnology Vol. 33; no. 5; pp. 531 - 537
Main Authors Zhang, Tianzhen, Hu, Yan, Jiang, Wenkai, Fang, Lei, Guan, Xueying, Chen, Jiedan, Zhang, Jinbo, Saski, Christopher A, Scheffler, Brian E, Stelly, David M, Hulse-Kemp, Amanda M, Wan, Qun, Liu, Bingliang, Liu, Chunxiao, Wang, Sen, Pan, Mengqiao, Wang, Yangkun, Wang, Dawei, Ye, Wenxue, Chang, Lijing, Zhang, Wenpan, Song, Qingxin, Kirkbride, Ryan C, Chen, Xiaoya, Dennis, Elizabeth, Llewellyn, Danny J, Peterson, Daniel G, Thaxton, Peggy, Jones, Don C, Wang, Qiong, Xu, Xiaoyang, Zhang, Hua, Wu, Huaitong, Zhou, Lei, Mei, Gaofu, Chen, Shuqi, Tian, Yue, Xiang, Dan, Li, Xinghe, Ding, Jian, Zuo, Qiyang, Tao, Linna, Liu, Yunchao, Li, Ji, Lin, Yu, Hui, Yuanyuan, Cao, Zhisheng, Cai, Caiping, Zhu, Xiefei, Jiang, Zhi, Zhou, Baoliang, Guo, Wangzhen, Li, Ruiqiang, Chen, Z Jeffrey
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.05.2015
Nature Publishing Group
Subjects
38/39
38/91
45/23
631/208/212/2304
631/208/2491/3933
631/449/711
631/61/514/2254
Agriculture
Base Sequence
Bioinformatics
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Chromosome Mapping
Cotton
Cotton Fiber
Crops
DNA sequencing
Domestication
Genome, Plant
Genomes
Gossypium - genetics
Gossypium hirsutum
High-Throughput Nucleotide Sequencing
Identification and classification
Life Sciences
Methods
Nucleotide sequencing
Plant Proteins - biosynthesis
Plant Proteins - genetics
Polyploidy
Sequence Analysis, DNA
Tetraploidy
Online AccessGet full text

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Abstract 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.
AbstractList 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.
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 theA 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.
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.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.
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.
Audience Academic
Author Wan, Qun
Wang, Dawei
Song, Qingxin
Stelly, David M
Cao, Zhisheng
Lin, Yu
Zhang, Hua
Jiang, Wenkai
Scheffler, Brian E
Tao, Linna
Dennis, Elizabeth
Fang, Lei
Zhang, Tianzhen
Zhang, Jinbo
Hu, Yan
Chang, Lijing
Ding, Jian
Cai, Caiping
Pan, Mengqiao
Zhou, Baoliang
Zhang, Wenpan
Thaxton, Peggy
Zuo, Qiyang
Zhou, Lei
Xiang, Dan
Jones, Don C
Wang, Sen
Chen, Xiaoya
Mei, Gaofu
Li, Ruiqiang
Chen, Jiedan
Hulse-Kemp, Amanda M
Tian, Yue
Hui, Yuanyuan
Zhu, Xiefei
Ye, Wenxue
Peterson, Daniel G
Wang, Qiong
Guan, Xueying
Wu, Huaitong
Saski, Christopher A
Xu, Xiaoyang
Jiang, Zhi
Liu, Bingliang
Li, Xinghe
Liu, Yunchao
Wang, Yangkun
Kirkbride, Ryan C
Liu, Chunxiao
Chen, Z Jeffrey
Guo, Wangzhen
Llewellyn, Danny J
Chen, Shuqi
Li, Ji
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  organization: Clemson University Genomics Institute, Clemson University
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  organization: Department of Soil and Crop Sciences, Texas A&M University
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  email: zjchen@austin.utexas.edu
  organization: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin
BackLink https://www.ncbi.nlm.nih.gov/pubmed/25893781$$D View this record in MEDLINE/PubMed
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Snippet Two draft sequences of Gossypium hirsutum, the most widely cultivated cotton species, provide insights into genome structure, genome rearrangement, gene...
Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1...
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SubjectTerms 38/39
38/91
45/23
631/208/212/2304
631/208/2491/3933
631/449/711
631/61/514/2254
Agriculture
Base Sequence
Bioinformatics
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Chromosome Mapping
Cotton
Cotton Fiber
Crops
DNA sequencing
Domestication
Genome, Plant
Genomes
Gossypium - genetics
Gossypium hirsutum
High-Throughput Nucleotide Sequencing
Identification and classification
Life Sciences
Methods
Nucleotide sequencing
Plant Proteins - biosynthesis
Plant Proteins - genetics
Polyploidy
Sequence Analysis, DNA
Tetraploidy
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Title Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
URI https://link.springer.com/article/10.1038/nbt.3207
https://www.ncbi.nlm.nih.gov/pubmed/25893781
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Volume 33
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