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Background   Xanthomonas fragariae  (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus  Xanthomonas , and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content.    Results  The Xf draft genome (4.2 Mb) was considerably smaller than most known  Xanthomonas  genomes (~5 Mb). Only half of the genes coding for  TonB -dependent transporters and cell-wall degrading enzymes that are typically present in other  Xanthomonas  genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii)  xcs , one of two Type II Secretion System coding regions in  Xanthomonas , and iv) the genes coding for the glyoxylate shunt pathway. Conversely, the Xf genome revealed a high content of externally derived DNA and several uncommon, possibly virulence-related features: a Type VI Secretion System, a second Type IV Secretion System and a distinct Type III Secretion System effector repertoire comprised of multiple rare effectors and several putative new ones.    Conclusions  The draft genome sequence of LMG 25863 confirms the distinct phylogenetic position of Xf within the genus  Xanthomonas  and reveals a patchwork of both lost and newly acquired genomic features. These features may help explain the specific, mostly endophytic association of Xf with the strawberry plant.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-14-829) contains supplementary material, which is available to authorized users.

Draft genome sequence of Xanthomonas fragariaereveals reductive evolution and distinct virulence-related gene content