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Background  The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are  x  = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between  Malus  (subfamily Maloideae) and  Prunus  (subfamily Prunoideae); however no data has been published to date comparing  Malus  or  Prunus  to a member of the subfamily Rosoideae. In this paper we compare the genome of  Fragaria , a member of the Rosoideae, to  Prunus , a member of the Prunoideae.    Results  The diploid genomes of  Prunus  ( 2n  =  2x  = 16) and  Fragaria  ( 2n  =  2x  = 14) were compared through the mapping of 71 anchor markers – 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) – on the reference maps of both genera. These markers provided good coverage of the  Prunus  (78%) and  Fragaria  (78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker in  Prunus  and 32 cM and 8.0 cM/marker in  Fragaria .    Conclusion  Our results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.

Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria(the strawberry)