title: Taxogenomics of the order Chlamydiales.
abstract: Bacterial classification is a long-standing problem for taxonomists and species definition itself is constantly debated among specialists. The classification of strict intracellular bacteria such as members of the order Chlamydiales mainly relies on DNA- or protein-based phylogenetic reconstructions because these organisms exhibit few phenotypic differences and are difficult to culture. The availability of full genome sequences allows the comparison of the performance of conserved protein sequences to reconstruct Chlamydiales phylogeny. This approach permits the identification of markers that maximize the phylogenetic signal and the robustness of the inferred tree. In this study, a set of 424 core proteins was identified and concatenated to reconstruct a reference species tree. Although individual protein trees present variable topologies, we detected only few cases of incongruence with the reference species tree, which were due to horizontal gene transfers. Detailed analysis of the phylogenetic information of individual protein sequences (i) showed that phylogenies based on single randomly chosen core proteins are not reliable and (ii) led to the identification of twenty taxonomically highly reliable proteins, allowing the reconstruction of a robust tree close to the reference species tree. We recommend using these protein sequences to precisely classify newly discovered isolates at the family, genus and species levels.
authors: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.|Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
authors: Trestan
authors: T
authors: Pillonel
authors: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.|Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
authors: Claire
authors: C
authors: Bertelli
authors: Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland.|SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors: Nicolas
authors: N
authors: Salamin
authors: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
authors: Gilbert
authors: G
authors: Greub
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics; D002695:Chlamydiales / Q000145:classification*; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000235:genetics; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S