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

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

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

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

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

Phylogenetic relationship of chlamydial pmp-family proteins.

<p>The maximum-likelihood tree is based on alignments of the conserved PMP_M middle domain and autotransporter domain. Species included in the tree are <i>C. psittaci</i> 6BC (CPS), <i>C. abortus</i> S26/3 (CAB), <i>C. felis</i> Fe/C-56 (CF) , <i>C. caviae</i> GPIC (CCA), <i>C. pneumoniae</i> LPCoLN (CPK), <i>C. muridarum</i> Nigg (TC) and <i>C. trachomatis</i> 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) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035097#pone.0035097-Grimwood1" target="_blank">[44]</a>. Bootstrap values are displayed at the branches. Pseudogenes are marked by .</p

Genes potentially under positive selection between <i>C. psittaci</i> and <i>C. abortus</i>.

<p>Genes potentially under positive selection between <i>C. psittaci</i> and <i>C. abortus</i>.</p

Global genome comparison between the <i>C. psittaci</i> 6BC, <i>C. abortus</i> S26/3, <i>C. felis</i> Fe/C-56, <i>C. pneumoniae</i> LPCoLN, and <i>C. trachomatis</i> L2/434/Bu genomes.

<p>The figure shows orthologous matches visualized using genoPlotR (compare <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035097#s3" target="_blank">Methods</a>). 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.</p