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

Abstract

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.

A chromosome-scale assembly for ‘d’Anjou’ pear

“…Therefore, we compared the genomes of 3 of these important crops: P. communis ‘d’Anjou’ (pear), M. domestica ‘Honeycrisp’ (apple ( Khan et al . 2022 )), and P. cerasus ‘Montmorency’ (cherry ( Goeckeritz et al . 2023 )).…”

Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring

“…For instance, a SQUAMOSA PROMOTER-BINDING LIKE gene ( SPL5 ), LFY , SUPPRESSOR OF OVEREXPRESSION OF CONSTANS ( SOC1 ), and PHOTOPERIOD INSENSITIVE EARLY-FLOWERING ( PIE1 ) have all been cherry-picked as candidates over the years (Moon et al ., 2003; Noh and Amasino, 2003; Silva et al ., 2005; Wu and Poethig, 2006; Dirlewanger et al ., 2012; Castede et al ., 2015). Fortunately, resources are rapidly being generated as genome sequencing becomes routine (Verde et al ., 2017; Jiang et al ., 2019; Wang et al ., 2020; Yi et al ., 2020; Cao et al ., 2022; Goeckeritz et al ., 2023 b ). Recently, researchers successfully fine-mapped a chromosome 4 QTL in P. avium (sweet cherry) to just 12 genes within a 68 kb region in the ‘Regina’ genome (Branchereau et al ., 2022).…”

“…Therefore, it is reasonable to suspect more than one major regulator of bloom time is present on Prunus chromosome 4. Further supporting multiple regulators is the finding that k is derived from subgenome A, a P. fruticosa -like subgenome (Bird et al ., 2022; Goeckeritz et al ., 2023 b ). Given the contrasting selective pressures in the native habitats of P. fruticosa and P. avium , we now have incentive to believe the bloom time variation in these species is conferred by separate genes.…”

“…Sour cherry is a recent allotetraploid with progenitors closely related to Prunus avium (sweet cherry) and Prunus fruticosa (ground cherry) (Olden and Nybom, 1968; Iezzoni and Hancock, 1984; Brettin et al ., 2000; Bird et al ., 2022). The recent publication of a reference genome for the cultivar Montmorency revealed three distinct subgenomes: A, A’, and B, with subgenome B at twice the dosage of A and A’ (Goeckeritz et al ., 2023 b ). The two copies of subgenome B were inherited from the P. avium -like ancestor while subgenomes A and A’ originated from the P. fruticosa -like ancestor, which was also shown to be an allotetraploid of two unknown Prunus species.…”

A landscape of resistance gene analogs in sour cherry (Prunus cerasus L.)

“…Plants possess an innate immune system that essentially consists of two branches [7] to defend against pathogens, one of which is based on the recognition of pathogens by resistance proteins encoded by R-genes in individual cells. The major classes of plant resistance genes are grouped based on their functional domains e.g.…”