A chromosome-scale assembly for tetraploid sour cherry (Prunus cerasusL.) ‘Montmorency’ identifies three distinct ancestralPrunusgenomes

Background Sour cherry ( Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors most closely related to extant P. fruticosa (ground cherry) and P. avium (sweet cherry). Sour cherry is an allotetraploid with few genomic resources, so a genome sequence would greatly facilitate the improvement of this crop. In Prunus , 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 of P. fruticosa to use alongside a published P. avium sequence 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 a P. fruticosa-like ancestor (A and A’) and two copies of the same subgenome inherited from a P. 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). The S -alleles and DAMs in ‘Montmorency’ and P. fruticosa were 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 genus Prunus . These genomic resources will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.