Table 1.
Summary of Chlamydiaceae genome features.
Figure 1.
Phylogenomic relationships among sequenced chlamydial genomes.
The maximum-likelihood tree is based on 100 randomly chosen conserved orthologous genes. Bootstrap values are displayed at the branches. The panels show the within-species phylogenetic relationships of the sequenced genomes of Chlamydia pneumoniae (upper panel) and C. trachomatis (lower panel).
Figure 2.
Venn diagrams showing the numbers of predicted CDSs that are unique or shared among two or more taxa.
A. Number of shared genes among the closely related C. psittaci, C. abortus, C. caviae, and C. felis; B. number of shared genes among the wider range of Chlamydiaceae. Pseudogenes were scored as absent in this analysis.
Figure 3.
Comparison of the plasticity zone of C. psittaci 6BC, C. abortus S26/3, C. felis Fe/C-56, C. caviae GPIC, C. pneumoniae LPCoLN and AR39, and C. trachomatis L2/434/Bu.
Genes are labelled with the published locus tag numbers. Colour-coded genes are discussed in the text. Pseudogenes are marked by .
Table 2.
Predicted CDSs unique to C. psittaci 6BC.
Table 3.
Comparison of predicted type III secreted proteins of C. psittaci 6BC with orthologs in other Chlamydiaceae.
Figure 4.
Global genome comparison between the C. psittaci 6BC, C. abortus S26/3, C. felis Fe/C-56, C. pneumoniae LPCoLN, and C. trachomatis L2/434/Bu genomes.
The figure shows orthologous matches visualized using genoPlotR (compare Methods). The grey tick marks above and below the sequence lines represent the predicted CDSs on the plus strand and the minus strand of the genomes, respectively. Colour-marked are (blue) members of the polymorphic membrane protein family (pmp) and (green) the position of the plasticity zone (PZ). The red lines connecting genome lines represent direct orthologous matches. The blue lines represent reversed matches. Darker colours correspond to a higher bit scores.
Figure 5.
Structure of the pmp-family proteins of C. psittaci 6BC.
Proteins are ordered by their position in the genome. The letter codes A to G/I indicate the pmp protein subfamilies as previously assigned by [44]. CPSIT_0314 has been reconstructed in silico. CPSIT_0300 is a gene remnant.
Figure 6.
Phylogenetic relationship of chlamydial pmp-family proteins.
The maximum-likelihood tree is based on alignments of the conserved PMP_M middle domain and autotransporter domain. Species included in the tree are C. psittaci 6BC (CPS), C. abortus S26/3 (CAB), C. felis Fe/C-56 (CF) , C. caviae GPIC (CCA), C. pneumoniae LPCoLN (CPK), C. muridarum Nigg (TC) and C. trachomatis L2/434/Bu (CTL). Pmps cluster into 6 major subfamilies previously designated A (orange), B/C (purple), D (red), E/F (blue), G/I (yellow), and H (green) [44]. Bootstrap values are displayed at the branches. Pseudogenes are marked by .
Figure 7.
Organization of the pmp-family proteins compared between C. psittaci 6BC, C. abortus S26/3, C. felis Fe/C-56, C. pneumoniae LPCoLN, and C. trachomatis L2/434/Bu.
Arrows indicate the gene orientation. The colour code denotes the membership to a pmp-subfamily. CDSs are designated by the numeric part of the published locus tags. Orthologous genes as inferred from the phylogenetic analysis shown in Figure 6, are connected by grey bars. Pseudogenes are marked by .
Figure 8.
Distributions of for orthologous genes from pairs of chlamydial genomes.
A. Distributions for comparisons among the closely related species C. psittaci, C. abortus, C. felis, and C. caviae. B. Distributions for comparisons among the more distantly related species C. psittaci and C. caviae vs. C. pneumoniae and C. trachomatis, respectively. As a point of reference the comparison C. psittaci vs. C. abortus is included in both plots. Probability density curves were estimated by Gaussian-kernel smoothing.
Figure 9.
Dependence of median on the genetic distance between genomes estimated as the median non-synonymous substitution rate,
.
Table 4.
Genes potentially under positive selection between C. psittaci and C. abortus.