The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins

Abstract. The presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the Bacteria. Using such indels, all of the main groups within the Bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: Low G+C Gram-positive → High G+C Gram-positive → Deinococcus–Thermus → Cyanobacteria → Spirochetes → Aquifex–Chlamydia–Cytophaga → Proteobacteria-1 (ε, δ) → Proteobacteria-2 (α)→ Proteobacteria-3 (β) → Proteobacteria -4 (γ). The usefulness of this approach for understanding bacterial phylogeny was examined here using sequence data from various completed bacterial genomes. By using 12 indels in highly conserved and widely represented proteins, the species from all 41 completed bacterial genomes were assigned to different groups; and the observed distribution of these indels in different species was then compared with that predicted by the signature sequence model. The presence or absence of these indels in various proteins in different bacteria followed the pattern exactly as predicted; and, in more than 450 observations, no exceptions or contradictions in the placement of indels were observed. These results provide strong evidence that lateral gene transfer events have not affected the genes containing these indels to any significant extent. The phylogenetic placement of bacteria into different groups based on signature sequences also showed an excellent correlation with the 16 S rRNA with 39 of the 41 species assigned to the same group by both methods. These results strongly vindicate the usefulness of the signature sequence approach to understanding phylogeny within the Bacteria and show that it provides a reliable and internally consistent means for the placement of bacterial species into different groups and for determining the relative branching order of the groups.