Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae.

The evolutionary relationships of Chlamydiales, Verrucomicrobia and Planctomycetes were studied based on phylogenetic trees for a concatenated dataset of 11 widely distributed proteins, as well as conserved inserts in several proteins. In phylogenetic trees, a close relationship of chlamydiae to Verrucomicrobium was supported by different phylogenetic methods. Although the Planctomycetes branched close to the chlamydiae-Verrucomicrobia clade, their specific affiliation to these groups was generally not supported. Results are also presented for two conserved inserts, a 6 aa insert in the lysyl-tRNA synthetase and a 3 aa insert in the RNA polymerase beta subunit (RpoB), that are uniquely shared by Verrucomicrobium spinosum and all available Chlamydiales homologues, but which are not found in any of the available Planctomycetes or other bacterial homologues. Signature sequences in a number of other proteins [including a large insert (>150 aa) in DNA gyrase B] provide information regarding the branching position of these groups relative to other bacterial phyla. A close and specific relationship of V. spinosum to the Chlamydiales species, seen both in phylogenetic trees and by means of uniquely shared inserts in protein sequences, strongly indicates that these two groups of species shared a common ancestor exclusive of all other known bacteria. These results suggest that Verrucomicrobia may be the closest free-living relatives of the parasitic chlamydiae.