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

Zhang, T; Hu, Y; Jiang, W; Fang, L; Guan, X; Chen, J; Zhang, J; Saski, CA; Scheffler, BE; Stelly, DM; Hulse-Kemp, AM; Wan, Q; Liu, B; Liu, C; Wang, S; Pan, M; Wang, Y; Wang, D; Ye, W; Chang, L; Zhang, W; Song, Q; Kirkbride, RC; Chen, X; Dennis, E; Llewellyn, DJ; Peterson, DG; Thaxton, P; Jones, DC; Wang, Q; Xu, X; Zhang, H; Wu, H; Zhou, L; Mei, G; Chen, S; Tian, Y; Xiang, D; Li, X; Ding, J; Zuo, Q; Tao, L; Liu, Y; Li, J; Lin, Y; Hui, Y; Cao, Z; Cai, C; Zhu, X; Jiang, Z; Zhou, B; Guo, W; Li, R; Chen, ZJ

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

Zhang, T Hu, Y Jiang, W Fang, L Guan, X Chen, J Zhang, J Saski, CA Scheffler, BE Stelly, DM Hulse-Kemp, AM Wan, Q Liu, B Liu, C Wang, S Pan, M Wang, Y Wang, D Ye, W Chang, L Zhang, W Song, Q Kirkbride, RC Chen, X Dennis, E

Llewellyn, DJ Peterson, DG Thaxton, P Jones, DC Wang, Q Xu, X Zhang, H Wu, H Zhou, L Mei, G Chen, S Tian, Y Xiang, D Li, X Ding, J Zuo, Q Tao, L Liu, Y Li, J Lin, Y Hui, Y Cao, Z Cai, C Zhu, X Jiang, Z Zhou, B Guo, W Li, R Chen, ZJ

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Publication Type:: Journal Article
Citation:: Nature Biotechnology, 2015, 33 (5), pp. 531 - 537
Issue Date:: 2015-05-12

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Field	Value	Language
dc.contributor.author	Zhang, T	en_US
dc.contributor.author	Hu, Y	en_US
dc.contributor.author	Jiang, W	en_US
dc.contributor.author	Fang, L	en_US
dc.contributor.author	Guan, X	en_US
dc.contributor.author	Chen, J	en_US
dc.contributor.author	Zhang, J	en_US
dc.contributor.author	Saski, CA	en_US
dc.contributor.author	Scheffler, BE	en_US
dc.contributor.author	Stelly, DM	en_US
dc.contributor.author	Hulse-Kemp, AM	en_US
dc.contributor.author	Wan, Q	en_US
dc.contributor.author	Liu, B	en_US
dc.contributor.author	Liu, C	en_US
dc.contributor.author	Wang, S	en_US
dc.contributor.author	Pan, M	en_US
dc.contributor.author	Wang, Y	en_US
dc.contributor.author	Wang, D	en_US
dc.contributor.author	Ye, W	en_US
dc.contributor.author	Chang, L	en_US
dc.contributor.author	Zhang, W	en_US
dc.contributor.author	Song, Q	en_US
dc.contributor.author	Kirkbride, RC	en_US
dc.contributor.author	Chen, X	en_US
dc.contributor.author	Dennis, E https://orcid.org/0000-0002-7850-591X	en_US
dc.contributor.author	Llewellyn, DJ	en_US
dc.contributor.author	Peterson, DG	en_US
dc.contributor.author	Thaxton, P	en_US
dc.contributor.author	Jones, DC	en_US
dc.contributor.author	Wang, Q	en_US
dc.contributor.author	Xu, X	en_US
dc.contributor.author	Zhang, H	en_US
dc.contributor.author	Wu, H	en_US
dc.contributor.author	Zhou, L	en_US
dc.contributor.author	Mei, G	en_US
dc.contributor.author	Chen, S	en_US
dc.contributor.author	Tian, Y	en_US
dc.contributor.author	Xiang, D	en_US
dc.contributor.author	Li, X	en_US
dc.contributor.author	Ding, J	en_US
dc.contributor.author	Zuo, Q	en_US
dc.contributor.author	Tao, L	en_US
dc.contributor.author	Liu, Y	en_US
dc.contributor.author	Li, J	en_US
dc.contributor.author	Lin, Y	en_US
dc.contributor.author	Hui, Y	en_US
dc.contributor.author	Cao, Z	en_US
dc.contributor.author	Cai, C	en_US
dc.contributor.author	Zhu, X	en_US
dc.contributor.author	Jiang, Z	en_US
dc.contributor.author	Zhou, B	en_US
dc.contributor.author	Guo, W	en_US
dc.contributor.author	Li, R	en_US
dc.contributor.author	Chen, ZJ	en_US
dc.date.available	2015-03-15	en_US
dc.date.issued	2015-05-12	en_US
dc.identifier.citation	Nature Biotechnology, 2015, 33 (5), pp. 531 - 537	en_US
dc.identifier.issn	1087-0156	en_US
dc.identifier.uri	http://hdl.handle.net/10453/118706
dc.description.abstract	© 2015 Nature America, Inc. All rights reserved. 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.	en_US
dc.relation.ispartof	Nature Biotechnology	en_US
dc.relation.isbasedon	10.1038/nbt.3207	en_US
dc.subject.mesh	Gossypium	en_US
dc.subject.mesh	Plant Proteins	en_US
dc.subject.mesh	Chromosome Mapping	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Base Sequence	en_US
dc.subject.mesh	Genome, Plant	en_US
dc.subject.mesh	Cotton Fiber	en_US
dc.subject.mesh	Tetraploidy	en_US
dc.subject.mesh	High-Throughput Nucleotide Sequencing	en_US
dc.title	Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement	en_US
dc.type	Journal Article
utslib.citation.volume	5	en_US
utslib.citation.volume	33	en_US
utslib.for	MD Multidisciplinary	en_US
utslib.for	060411 Population, Ecological and Evolutionary Genetics	en_US
utslib.for	0703 Crop and Pasture Production	en_US
utslib.for	0607 Plant Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	closed_access
pubs.issue	5	en_US
pubs.publication-status	Published	en_US
pubs.volume	33	en_US

Abstract:

© 2015 Nature America, Inc. All rights reserved. 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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/118706