Genome of tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes.

Sour cherry ( L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant (ground cherry) and (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the USA. We also generated a draft assembly of to use alongside a published sequence for syntelog-based subgenome assignments for 'Montmorency' and provide compelling evidence is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show 'Montmorency' is trigenomic, containing two distinct subgenomes inherited from a -like ancestor (A and A') and two copies of the same subgenome inherited from a -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 , two known classes of genes are important to breeding strategies: the self-incompatibility loci (alleles), which determine compatible crosses, successful fertilization, and fruit set, and the genes (), which strongly affect dormancy transitions and flowering time. The -alleles and in 'Montmorency' and 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 and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.