title: Genus delineation of Chlamydiales by analysis of the percentage of conserved proteins justifies the reunifying of the genera Chlamydia and Chlamydophila into one single genus Chlamydia.
abstract: Many studies have aimed to set up boundaries for the classification and definition of prokaryotic genus and species classification; however, studies that focused on genus-level genomic differences for existing taxonomy systems are limited. Recently, a novel method was described for prokaryotic genus delineation using the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance (Qin et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196: :2210-5). Here, we extended the POCP analysis of the order Chlamydiales and pairwise compared all currently recognized species and candidate species of the family Chlamydiaceae as well as some species from other families. Using the taxonomy advised by the International Committee on Systematics of Prokaryotes, subcommittee on the taxonomy of the Chlamydiae, POCP analysis revealed that all pairwise comparisons of species from different families resulted in values lower than 50%, the proposed threshold for genus boundary. In contrast, all interspecies pairwise comparisons of species from the single genus within the family Chlamydiaceae resulted in POCP values higher than 70%. We conclude that the recommended genus classification of the family Chlamydiaceae is rational and that POCP analyses can provide a robust genomic index for the taxonomy of members of the order Chlamydiales in terms of genus demarcation.
authors.affiliation: Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Center, Amsterdam, The Netherlands y.pannekoek@amc.uva.nl.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Pannekoek
authors.affiliation: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China Marine Biotechnology Research Center, Shandong University, Jinan, China Institute of Marine Science and Technology, Shandong University, Jinan, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Qi-Long
authors.affiliation: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China Marine Biotechnology Research Center, Shandong University, Jinan, China Institute of Marine Science and Technology, Shandong University, Jinan, China.
authors.forename: Yu-Zhong
authors.initials: YZ
authors.lastname: Zhang
authors.affiliation: Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: Arie
authors.initials: A
authors.lastname: van der Ende
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D002689:Chlamydia / Q000145:classification* / Q000235:genetics*; D002695:Chlamydiales / Q000145:classification* / Q000235:genetics*; D023501:Chlamydophila / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D017124:Conserved Sequence; D019143:Evolution, Molecular; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S
keywords: Chlamydia; Chlamydiaceae; Chlamydiales; POCP; phylogeny; taxonomy