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Trees with weeping shoot architectures are valued for their beauty and serve as tremendous resources for understanding how plants regulate posture control. ThePrunus persica(peach) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in theWEEPgene. Until now, little was known about the function of WEEP protein despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach does not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development.This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster root gravitropic response, just as barley and wheat with mutations in theirWEEPhomologEGT2. This suggests that the role of WEEP in regulating lateral organ angles and orientations during gravitropism may be conserved. Additionally, size-exclusion chromatography indicated that WEEP proteins self-oligomerize, like other SAM-domain proteins. This oligomerization may be required for WEEP to function in formation of protein complexes during auxin transport. Collectively, our results from weeping peach provide new insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.

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.

BackgroundSour 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.ResultsHere 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-likeancestor (A and A’) and two copies of the same subgenome inherited from aP. avium-likeancestor (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.ConclusionsThe 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.