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Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

Wang, M.; Tu, L.; Yuan, D.; Zhu, D.; Shen, C.; Li, J.; Liu, F.; Pei, L.; Wang, P.; Zhao, G.; Ye, Z.; Huang, H.; Yan, F.; Ma, Y.; Zhang, L.; Liu, M.; You, J.; Yang, Y.; Liu, Z.; Huang, F.; Li, B.; Qiu, P.; Zhang, Q.; Zhu, L.; Jin, S.; Yang, X.; Min, L.; Li, G.; Chen, L.-L.; Zheng, H.; Lindsey, K.; Lin, Z.; Udall, J.A.; Zhang, X.

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense Thumbnail


M. Wang

L. Tu

D. Yuan

D. Zhu

C. Shen

J. Li

F. Liu

L. Pei

P. Wang

G. Zhao

Z. Ye

H. Huang

F. Yan

Y. Ma

L. Zhang

M. Liu

J. You

Y. Yang

Z. Liu

F. Huang

B. Li

P. Qiu

Q. Zhang

L. Zhu

S. Jin

X. Yang

L. Min

G. Li

L.-L. Chen

H. Zheng

Z. Lin

J.A. Udall

X. Zhang


Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1,2,3,4. Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3–79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes1,3, these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement.


Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J., …Zhang, X. (2019). Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics, 51, 224-229.

Journal Article Type Article
Acceptance Date Oct 19, 2018
Online Publication Date Dec 3, 2018
Publication Date Feb 1, 2019
Deposit Date Dec 4, 2018
Publicly Available Date Feb 1, 2019
Journal Nature Genetics
Print ISSN 1061-4036
Electronic ISSN 1546-1718
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 51
Pages 224-229


Published Journal Article (Advance online version) (2 Mb)

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Copyright Statement
Advance online version © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation,<br /> distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to<br /> the Creative Commons license, and indicate if changes were made. Te images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in<br /> the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.<br /> org/licenses/by/4.0/.

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