A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes

• DOI: 10.1093/g3journal/jkae080
• Publication Date: 2024-04-12T18:14:12Z
• Authors: Awie J Hosaka; Rena Sanetomo; Kazuyoshi Hosaka
• Keywords: Synteny; Genome size; Sequence assembly

Abstract Potato and its wild relatives are distributed mainly in the Mexican highlands central Andes of South America. The American A-genome species, including cultivated potatoes, reproductively isolated from diploid species. Whole-genome sequencing has disclosed genome structure similarity, mostly potatoes their closely related In this study, we generated a chromosome-scale assembly Solanum bulbocastanum Dun., using PacBio long-read sequencing, optical mapping, Hi-C scaffolding technologies. final sequence consisted 737.9 Mb, among which 647.0 Mb were anchored to 12 chromosomes. Compared with assemblies S. lycopersicum (tomato), etuberosum (non-tuber-bearing species E-genome), verrucosum, chacoense, multidissectum, phureja (all four species), bulbocastnum was shortest. It contained fewer transposable elements (56.2%) than A cluster analysis performed based on pairwise ratios syntenic regions seven assemblies, showing that first clustered as distinct group. Then, group bulbocastanum. Sequence similarity 1,624 single-copy orthologous gene groups 36 clones separated specific group, other Therefore, differs sequences These findings provide important insights into understanding utilizing genetic diversity potato breeding.