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

Authors: Wang, Maojun and Tu, Lili and Yuan, Daojun and Zhu, De and Shen, Chao and Li, Jianying and Liu, Fuyan and Pei, Liuling and Wang, Pengcheng and Zhao, Guannan and Ye, Zhengxiu and Huang, Hui and Yan, Feilin and Ma, Yizan and Zhang, Lin and Liu, Min and You, Jiaqi and Yang, Yicheng and Liu, Zhenping and Huang, Fan and Li, Baoqi and Qiu, Ping and Zhang, Qinghua and Zhu, Longfu and Jin, Shuangxia and Yang, Xiyan and Min, Ling and Li, Guoliang and Chen, Ling-Ling and Zheng, Hongkun and Lindsey, Keith and Lin, Zhongxu and Udall, Joshua A and Zhang, Xianlong

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 incomplete1-4. 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.

Journal: Nature genetics
DOI: 10.1038/s41588-018-0282-x
Year: 2019

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