A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy

The genus Prunus, which contains 250–400 species, has ample genomic resources for the economically important taxa in group including cherries, peaches, and almonds. However, backbone of specifically position racemose relative to solitary corymbose groups, remains phylogenetically uncertain. Surprisingly, phylogenomic analyses resolve relationships are lacking. Here, we assemble transcriptomes from 17 Prunus species representing four subgenera, use existing transcriptome assemblies, key using a approach. From transcriptomes, constructed 21-taxon datasets putatively single-copy nuclear genes with 591 379 genes, depending on taxon-occupancy filtering. Plastome sequences were obtained or assembled all present data set. was resolved consistently chloroplast phylogenies, but found substantial cytonuclear discord within subgenera. Our phylogeny recovered monophyletic group, contrasting previous studies finding paraphyly that suggests repeated allopolyploidy early evolutionary history genus. detected multiple histories consistent hybridization allopolyploidy, deep event involving subgenus Amygdalus Armeniaca clade Prunus. Analyses gene tree conflict revealed at several nodes, crown node group. Alternative topologies conflicted paraphyletic highlighting complex reticulated this