title: A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.
abstract: The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated.
authors.affiliation: INRA, UR0407 Pathologie Végétale, Montfavet, France.
authors.forename: Odile
authors.initials: O
authors.lastname: Berge
authors.affiliation: INRA, UR0407 Pathologie Végétale, Montfavet, France.
authors.forename: Caroline L
authors.initials: CL
authors.lastname: Monteil
authors.affiliation: INRA, UR0407 Pathologie Végétale, Montfavet, France; Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), Tuscia University, Viterbo, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Bartoli
authors.affiliation: INRA, UR0407 Pathologie Végétale, Montfavet, France.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Chandeysson
authors.affiliation: INRA, UR0407 Pathologie Végétale, Montfavet, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Guilbaud
authors.affiliation: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America.
authors.forename: David C
authors.initials: DC
authors.lastname: Sands
authors.affiliation: INRA, UR0407 Pathologie Végétale, Montfavet, France; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America.
authors.forename: Cindy E
authors.initials: CE
authors.lastname: Morris
mesh_terms: D001483:Base Sequence; D002950:Citrate (si)-Synthase / Q000235:genetics*; D030541:Databases, Genetic; D017753:Ecosystem; D005798:Genes, Bacterial; D020043:Genes, Essential; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010641:Phenotype; D010802:Phylogeny; D044224:Pseudomonas syringae / Q000145:classification / Q000235:genetics
chemical_list: D002950:Citrate (si)-Synthase