Haplotype-resolved chromosome-level genome assemblies of nineteen apple (Malus domestica Borkh.) cultivars

Apple (Malus domestica Borkh.) is a major fruit crop with a rich genetic history shaped by whole-genome duplication, domestication, and selective breeding. Discovering apple genetic diversity through genome sequencing provides new opportunities to improve disease resistance, environmental adaptation, and fruit quality. Here, we present 19 haplotype-resolved genome assemblies of apple, sequenced using PacBio HiFi reads with approximately 30 × coverage. Each haplome assembly has a mean length of 675.3 Mb and contains on average 47,445 annotated protein-coding genes. These haplome assemblies have a high completeness, with mean complete BUSCO scores of 98.8%. We identified 578 previously uncharacterized orthogroups shared across all 38 haplomes, indicating that these assemblies capture novel genetic diversity. Many of the assemblies are also highly contiguous, with on average three to four phase switches per chromosome. These data will accelerate genome-wide association studies, helping researchers to find and use genetic diversity for the improvement of key traits. Additionally, these data can offer insights into evolutionary history, domestication, and genetic diversity, supporting apple breeding and the broader Rosaceae research community.