title: Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content.
abstract: 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.
authors.affiliation: Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium. martine.maes@ilvo.vlaanderen.be.
authors.forename: Joachim
authors.initials: J
authors.lastname: Vandroemme
authors.forename: Bart
authors.initials: B
authors.lastname: Cottyn
authors.forename: Steve
authors.initials: S
authors.lastname: Baeyen
authors.forename: Paul
authors.initials: P
authors.lastname: De Vos
authors.forename: Martine
authors.initials: M
authors.lastname: Maes
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D058947:Bacterial Secretion Systems / Q000235:genetics; D001427:Bacterial Toxins / Q000235:genetics; D001483:Base Sequence; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D026901:Membrane Transport Proteins / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics; D014974:Xanthomonas / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D001427:Bacterial Toxins; D026901:Membrane Transport Proteins; D037521:Virulence Factors