Comparative Genome Analysis of 33 Strains Reveals Characteristic Features of and Closely Related Species.

To identify genome-based features characteristic of the avian and human pathogen and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in ), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in and as closest relatives), (iii) a 502-aa SinC protein, the largest among spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in 14 in C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual spp.