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

• DOI: 10.1038/s41467-022-28362-0
• Publication Date: 2022-02-03T11:07:29Z
• Authors: 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; Zhonghua Zhang
• Keywords: Cucumis

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