Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutumand Gossypium barbadense

First author: Maojun Wang; Affiliations: Huazhong Agricultural University (华中农业大学): Wuhan, China

Corresponding author: Xianlong Zhang

Allotetraploid cotton species (Gossypium hirsutum 陆地棉 and Gossypium barbadense 海岛棉) 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 incomplete. 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 genomes, 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.

异源四倍体棉花陆地棉和海岛棉作为自然可再生的纺织纤维来源具有较长的栽培历史。这两个棉花的基因组均已报道，但都片段化严重，不完整。本文通过整合单分子实时测序、BioNano光学图谱和Hi-C测序技术，报道了这两个种的参考级基因组组装和注释结果。与之前的基因组草图相比，本文所报道的基因组在着丝粒等高重复区域DNA片段的连续性和完整性上均有了很大幅度的提升。比较基因组学分析鉴定了很多的结构变异，并且这些变异极有可能是发生在多倍化之后，在14个染色体上存在大片段的臂间或臂内倒位。作者构建了一个渐渗系群体用来将海岛棉中感兴趣的染色体片段引入到陆地棉种，作者基于这个群体鉴定到了13个与纤维质量相关的数量性状位点。本文所报道的遗传资源将会加速棉花的演化和功能基因组学研究，并且加快未来棉花纤维改良的育种项目。

通讯：张献龙 (http://cpst.hzau.edu.cn/szdw/jsml/js/201702/t20170221_100933.htm)

个人简介：1980.09-1984.06，华中农业大学，作物遗传育种，学士；1984.09-1987.06，华中农业大学，作物遗传育种，硕士；1987.09-1990.06，华中农业大学，作物遗传育种，博士；1993.10-1994.10，加拿大曼尼托巴大学，农学院植物科学技术系，访问学者；1998.11-1999.04，美国阿拉巴马农工大学，植物科学系，访问学者；2001.11-2002.02，英国杜伦大学，生物系，访问学者。

研究方向：棉花生物技术及育种应用研究。

doi: https://doi.org/10.1038/s41588-018-0282-x

Journal: Nature Genetics

Published date: 03 December, 2018