Planctomycetes, Verrucomicrobia, and Chlamydiae in the traditional molecular phylogeny view are considered as phyla and also cluster together in what is referred to as the PVC superphylum, along with the candidate phyla Omnitrophica (previously OP3) and the Poribacteria. An important molecular marker in the form of a conserved signature protein has been found to be consistently shared by PVC members, with the exception of Poribacteria. The conserved signature protein may be a marker that represents a synapomorphic quality and a means to distinguish this bacterial group. Recent studies have characterized this protein and it has been attributed to play an important housekeeping function in DNA/RNA binding. This observation not only provides a means to demarcate the PVC superphylum, but it supports strongly supports an evolutionary relationship shared by this clade that is distinct from other bacteria.
Conserved signature indels (CSIs) have also been found specific for the Planctomycetes, Verrucomicrobia, and Chlamydiae that distinguish each respective phylum from one another, and from other bacteria. A three-amino-acid insert in the RNA polymerase protein RpoB has been found that is shared by all sequenced Verrucomicrobia, Chlamydiae, and Lentisphaerae species. The CSI is absent from neighbouring Planctomycetes' and Poribacteria, suggesting common ancestry among the groups for which the CSI is specific.
Additional lines of evidence for the existence of this clade have been found. These include the presence of membrane coat-like proteins, tubulin, sterol synthesis, and the presence of condensed DNA.
^ abWagner, M.; Horn, M. (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Current Opinion in Biotechnology. 17 (3): 241–249. doi:10.1016/j.copbio.2006.05.005. PMID16704931.
^ abCavalier-Smith, T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 7–76. doi:10.1099/00207713-52-1-7. PMID11837318.
^Forterre, Patrick (January 2011). "A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong". Research in Microbiology. 162 (1): 77–91. doi:10.1016/j.resmic.2010.10.005. PMID21034817.
^Wagner, M.; Horn, M. (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Current Opinion in Biotechnology. 17 (3): 241–249. doi:10.1016/j.copbio.2006.05.005. PMID16704931.
^Gupta RS, Naushad S, Chokshi C, Griffiths E, Adeolu M (2015). "A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia". Antonie van Leeuwenhoek. 108 (3): 765–781. doi:10.1007/s10482-015-0532-1. PMID26179278.
^Wagner M, Horn M (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance". Curr. Opin. Biotechnol. 17 (3): 241–9. doi:10.1016/j.copbio.2006.05.005. PMID16704931.