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Figure 4 | BMC Molecular Biology

Figure 4

From: Francisella RNA polymerase contains a heterodimer of non-identical α subunits

Figure 4

Phylogenetic trees of the bacterial RpoA. A. A set of 368 RpoA sequences from 355 representative genomes was aligned using MUSCLE program. The Maximum likelihood tree with bootstrap values applied was built for 246 informative aligned positions using FastTree program. B. A set of 84 RpoA sequences from 76 representative genomes of γ- and β-proteobacteria was aligned using MUSCLE program. The Maximum likelihood tree with bootstrap values applied was built for 296 aligned informative positions using RAxML program. The evolutionary model for tree reconstruction (WAG with gamma-distributed evolutionary rates) has been selected using ProtTest program. Colour code: light blue - RpoA1 subunits encoded in ribosomal operons, the default location for all bacteria; light green - RpoA2 subunits encoded elsewhere in the genome. Dashed arrows point to subtrees with two other (non-Francisella) instances of RpoA duplication: Chloroflexus species and Streptomyces avermitilis. Each terminal tree node is labelled with GenBank Identifier (GI) number, five-letter taxonomy code and full systematic name of an organism. The taxonomy code is the following: Gamma - γ-proteobacteria; Beta - β-proteobacteria; Alpha -α- proteobacteria; Clost - Clostridia; Dicty - Dictyoglomi; Deino -Deinococcus/Thermus group; Syner - Synergistetes; Nitro - Nitrospirae; Therm -Thermomicrobia; Dehal - Dehalococcoidetes; Fibro - Fibrobacteres/Acidobacteria group; Gemma - Gemmatimonadetes; uncla - unclassified. Compressed branches (black triangles) are labelled according to taxonomy. Branches leading to γ-proteobacteria are red. The shaded clade indicates close relatives of Fransicella according to taxonomy based on 16S rRNA and concatenated ribosomal proteins phylogeny.

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