Consulting Editors

Supplementary material 2 (DOCX 19 kb

Summary of <i>Chlamydiaceae</i> genome features.

<p>Summary of <i>Chlamydiaceae</i> genome features.</p

Venn diagrams showing the numbers of predicted CDSs that are unique or shared among two or more taxa.

<p><b>A.</b> Number of shared genes among the closely related <i>C. psittaci</i>, <i>C. abortus</i>, <i>C. caviae</i>, and <i>C. felis</i>; <b>B.</b> number of shared genes among the wider range of <i>Chlamydiaceae</i>. Pseudogenes were scored as absent in this analysis.</p

Distributions of for orthologous genes from pairs of chlamydial genomes.

<p><b>A.</b> Distributions for comparisons among the closely related species <i>C. psittaci</i>, <i>C. abortus</i>, <i>C. felis</i>, and <i>C. caviae</i>. <b>B.</b> Distributions for comparisons among the more distantly related species <i>C. psittaci</i> and <i>C. caviae</i> vs. <i>C. pneumoniae</i> and <i>C. trachomatis</i>, respectively. As a point of reference the comparison <i>C. psittaci</i> vs. <i>C. abortus</i> is included in both plots. Probability density curves were estimated by Gaussian-kernel smoothing.</p

Structure of the pmp-family proteins of <i>C. psittaci</i> 6BC.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035097#pone.0035097-Grimwood1" target="_blank">[44]</a>. CPSIT_0314 has been reconstructed <i>in silico</i>. CPSIT_0300 is a gene remnant.</p

Phylogenomic relationships among sequenced chlamydial genomes.

<p>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 <i>Chlamydia pneumoniae</i> (upper panel) and <i>C. trachomatis</i> (lower panel).</p

Dependence of median on the genetic distance between genomes estimated as the median non-synonymous substitution rate, .

<p>Dependence of median on the genetic distance between genomes estimated as the median non-synonymous substitution rate, .</p

Predicted CDSs unique to <i>C. psittaci</i> 6BC.

1<p>predicted T3S effector protein.</p

Comparison of the plasticity zone of <i>C. psittaci</i> 6BC, <i>C. abortus</i> S26/3, <i>C. felis</i> Fe/C-56, <i>C. caviae</i> GPIC, <i>C. pneumoniae</i> LPCoLN and AR39, and <i>C. trachomatis</i> L2/434/Bu.

<p>Genes are labelled with the published locus tag numbers. Colour-coded genes are discussed in the text. Pseudogenes are marked by .</p

Comparison of predicted type III secreted proteins of <i>C. psittaci</i> 6BC with orthologs in other <i>Chlamydiaceae</i>.

<p>Orthologs predicted to be type three secreted are represented with *.</p><p>Only genes with an SVM decision value >0.5 are reported as candidate type III secreted proteins <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035097#pone.0035097-Wang1" target="_blank">[18]</a>.</p><p>ORFs hightlighted in gray have also been predicted as T3SEs by EffectiveT3 ( <a href="http://effectors.org" target="_blank">http://effectors.org</a> ).</p