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

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 identific

SUBMITTER: Li H 

PROVIDER: S-EPMC8813957 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature