Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber

Hongbo Li, Shenhao Wang, Sen Chai, Zhiquan Yang, Qiqi Zhang, Hongjia Xin, Yuanchao Xu, Shengnan Lin, Xinxiu Chen, Zhiwang Yao, Qingyong Yang, Zhangjun Fei, Sanwen Huang and Zhonghua Zhang ()
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Hongbo Li: Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Shenhao Wang: Northwest A&F University
Sen Chai: Qingdao Agricultural University
Zhiquan Yang: Huazhong Agricultural University
Qiqi Zhang: Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Hongjia Xin: Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Yuanchao Xu: Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Shengnan Lin: Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Xinxiu Chen: Qingdao Agricultural University
Zhiwang Yao: Qingdao Agricultural University
Qingyong Yang: Huazhong Agricultural University
Zhangjun Fei: Cornell University
Sanwen Huang: Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences
Zhonghua Zhang: Qingdao Agricultural University

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.

Date: 2022
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DOI: 10.1038/s41467-022-28362-0

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