Societal impact statement Sour cherry (Prunus cerasus L.) is an agriculturally valuable tree that produces fruits used in a range of culinary dishes, beverages, and other products. The progenitor species and number of origins of sour cherry remain unresolved. Here, we performed phylogenetic analyses of plastid genomes and nuclear genes from nine wild species and three historically important sour cherry cultivars. Our analyses identified Prunus fruticosa and Prunus avium as the closest extant relatives of the progenitor species of tetraploid sour cherry. Furthermore, our analyses revealed P. fruticosa as the likely maternal contributor. These findings and transcriptomic datasets should serve as valuable new resources to guide future breeding efforts in sour cherry.

Sour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant P. fruticosa (ground cherry) and P. avium (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the U.S. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for ‘Montmorency’ and provide compelling evidence P. fruticosa is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show ‘Montmorency’ is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A’) and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). The genome composition of ‘Montmorency’ is AA’BB and little-to-no recombination has occurred between progenitor subgenomes (A/A’ and B). In Prunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. The S-alleles and DAMs in ‘Montmorency’ and P. fruticosa were manually-annotated and support subgenome assignments. Lastly, the hybridization event ‘Montmorency’ is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The ‘Montmorency’ genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.

Background: Sour cherry (Prunus cerasusL.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors most closely related to extantP. fruticosa(ground cherry) andP. avium(sweet cherry). Sour cherry is an allotetraploid with few genomic resources, so a genome sequence would greatly facilitate the improvement of this crop. InPrunus, two known classes of genes are of particular importance to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses and are critically important for successful fertilization and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. Results: Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant sour cherry cultivar grown in the U.S. We also generated a draft assembly ofP. fruticosato use alongside a publishedP. aviumsequence for syntelog-based subgenome assignments for ′Montmorency′. Using hierarchal k-mer clustering and phylogenomics, we provide compelling evidence this allotetraploid is trigenomic, containing two distinct subgenomes inherited from aP. fruticosa-like ancestor (A and A′) and two copies of the same subgenome inherited from aP. avium-like ancestor (BB). We therefore assigned the genome composition of ′Montmorency′ to be AA′BB and show little to no recombination has occurred between progenitor subgenomes (A/A′ and B). TheS-alleles and DAMs in ′Montmorency′ andP. fruticosawere manually annotated and demonstrated to support the three subgenome assignments. Lastly, the hybridization event that ′Montmorency′ is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. Conclusions: The genome of sour cherry cultivar Montmorency highlights the evolutionary complexity of the genusPrunus. These genomic resources will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.