Structural Variation and Resistance Gene Evolution in Octoploid Strawberry Revealed by High-Quality Genome Assemblies of ‘Suhong’ and ‘Earligrow’

Strawberry (Fragaria × ananassa) is an economically important crop. Recent advances in long-range sequencing technologies have enabled high-precision chromosome-level genome assembly. In Korea, reference genomes of the cultivars ‘Wongyo 3115’ and ‘Seolhyang’ have been constructed and are being utilized in precision breeding research. In this study, we report the high-quality chromosome-level genome assemblies of two cultivars, ‘Suhong’ and ‘Earligrow’, showing resistance to multiple diseases, including Fusarium wilt, powdery mildew, and anthracnose. Approximately 100 Gb of high-fidelity (HiFi) sequencing data were generated for each cultivar using the PacBio Revio platform, and gene prediction and functional annotation were performed based on these data. Comparative genomic analysis with previously reported octoploid strawberry cultivars revealed extensive structural variations, including inversions and translocations. NBS-LRR resistance gene searches using NLGenomeSweeper identified 730–753 candidate genes across both cultivars. The expansion of the TNL and NL subgroups reflects the important roles of polyploidization and gene duplication in the evolution of resistance genes. Selection pressure analysis revealed that TNL and CNL genes were under diversifying selection, whereas RNL genes were highly conserved. The results of this study highlight that ‘Suhong’ and ‘Earligrow’ are promising genetic resources for strawberry disease resistance breeding, and the constructed reference genomes are expected to serve as important foundational data for the discovery of resistance genes and the development of disease-resistant cultivars.