Figure 2

Comparative analysis of C. pecorum . (A) Whole genome comparison between C. pecorum strains PV3056/3, P787 and W73 and reference strain E58 [CP002608] showing ACT comparison of amino acid matches between complete 6-frame translations (computed using tblastx). Grey bars represent the forward and reverse strands of DNA with CDSs marked as arrows. The scale is marked in base pairs. The red bars represent individual tblastx matches. Inverted matches are coloured blue. (B) Maximum-likelihood (PhyML) phylogenetic tree calculated using a JTT + G substitution model with the concatenated sequences of 48 ribosomal proteins from species of the family Chlamydiaceae (an outgroup comprising sequences from other Chlamydiales family members is included). Bootstrap proportion values are indicated at the node. The scale bar indicates 0.1 expected substitutions per site. (C) Whole genome comparison of amino acid matches between C. pecorum PV3056/3, C. psittaci 6BC [CP002586] and C. pneumoniae AR39 [AE002161] showing ACT comparison of amino acid matches between complete 6-frame translations (computed using tblastx). Grey bars represent the forward and reverse strands of DNA with CDS encoding products marked as black arrows. The scale is marked in base pairs. The red bars represent individual tblastx matches. Inverted matches are coloured blue. The plasticity zone (PZ) is indicated.