Chromosome-scale genome assembly of the Santina and Regina varieties of Prunus avium

Recent advances in third-generation sequencing have enabled high-quality genome assemblies of complex plant genomes. Existing reference genomes of Prunus avium L. (sweet cherry) may not adequately represent the genetic diversity of the self-incompatible cultivars that are widely grown in Chile. We report chromosome-scale consensus and phased genome assemblies of two of the most cultivated varieties in Chile, ’Santina’ and ‘Regina’. This was achieved using a multi-platform strategy that combines PacBio HiFi, Nanopore, Hi-C, and a genetic map of sweet cherry. The assemblies span 354 Mbp (Santina) and 357.5 Mbp (Regina) and have contig N50 values of 22.7 Mbp and 19.2 Mbp, respectively. Chromosome anchoring covered 301 Mbp (85%) for Santina and 290.1 Mbp (82.5%) for Regina. BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis indicated high completeness (99.1–99.2%). Structural annotation based on mRNA Iso-Seq data identified 31,209 genes and 35,001 isoforms in Regina and 31,726 genes and 35,280 isoforms in Santina. The use of Iso-Seq data greatly improved transcript resolution and structural annotation. These assemblies represent the most complete and functionally annotated genomes of P. avium to date and provide valuable resources for the genetics and breeding of sweet cherry.