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Background  The Rosaceae family encompasses numerous genera exhibiting morphological diversification in fruit types and plant habit as well as a wide variety of chromosome numbers. Comparative genomics between various Rosaceous genera has led to the hypothesis that the ancestral genome of the family contained nine chromosomes, however, the synteny studies performed in the Rosaceae to date encompass species with base chromosome numbers  x  = 7 ( Fragaria ),  x  = 8 ( Prunus ), and  x  = 17 ( Malus ), and no study has included species from one of the many Rosaceous genera containing a base chromosome number of  x  = 9.    Results  A genetic linkage map of the species  Physocarpus opulifolius  ( x  = 9) was populated with sequence characterised SNP markers using genotyping by sequencing. This allowed for the first time, the extent of the genome diversification of a Rosaceous genus with a base chromosome number of  x  = 9 to be performed. Orthologous loci distributed throughout the nine chromosomes of  Physocarpus  and the eight chromosomes of  Prunus  were identified which permitted a meaningful comparison of the genomes of these two genera to be made.    Conclusions  The study revealed a high level of macro-synteny between the two genomes, and relatively few chromosomal rearrangements, as has been observed in studies of other Rosaceous genomes, lending further support for a relatively simple model of genomic evolution in Rosaceae.    Electronic supplementary material  The online version of this article (doi:10.1186/s13104-016-2069-4) contains supplementary material, which is available to authorized users.

Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus