title: Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity.
abstract: BACKGROUND
  Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains.
  
  
  RESULTS
  These distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences.
  
  
  CONCLUSIONS
  This extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation.
authors.affiliation: CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France. flt.ailloud@gmail.com.|Anses - Plant Health Laboratory, F-97410, Saint-Pierre, La Réunion, France. flt.ailloud@gmail.com.
authors.forename: Florent
authors.initials: F
authors.lastname: Ailloud
authors.affiliation: Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA. tiff.lowe@gmail.com.
authors.forename: Tiffany
authors.initials: T
authors.lastname: Lowe
authors.affiliation: Anses - Plant Health Laboratory, F-97410, Saint-Pierre, La Réunion, France. gilles.cellier@anses.fr.
authors.forename: Gilles
authors.initials: G
authors.lastname: Cellier
authors.affiliation: Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA), Evry, Paris, France. droche@genoscope.cns.fr.
authors.forename: David
authors.initials: D
authors.lastname: Roche
authors.affiliation: Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA. cza@plantpath.wisc.edu.
authors.forename: Caitilyn
authors.initials: C
authors.lastname: Allen
authors.affiliation: CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France. philippe.prior@cirad.fr.|Département de Santé des Plantes et Environnement, (SPE) Inra, Paris, France. philippe.prior@cirad.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Prior
mesh_terms: D060146:Ecotype; D005798:Genes, Bacterial; D023281:Genomics; D058507:Host Specificity; D028521:Musa / Q000382:microbiology; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D010944:Plants / Q000382:microbiology; D011110:Polymorphism, Genetic; D043368:Ralstonia solanacearum / Q000235:genetics* / Q000472:pathogenicity; D037521:Virulence Factors / Q000235:genetics
chemical_list: D037521:Virulence Factors