Applications of conserved indels and signature proteins for microbial phylogeny

Most prokaryotic taxa (genus level and above) are presently distinguished from each other mainly on the basis of their branching in the 16S rRNA and other phylogenetic trees. In most cases, no molecular, biochemical or physiological characteristics are known that are specific for species from these taxa and can be used to clearly demarcate them. Genome sequences provide a powerful resource for discovering new markers that are helpful in reliably distinguishing different groups of prokaryotes in molecular terms and for understanding their evolutionary relationships. Using genome sequence data, my group has pioneered the discovery of two kinds of molecular markers that are distinctive characteristics of different groups of organisms. These markers are comprised of either whole genes/proteins, or conserved indels (i.e. inserts or deletions) in widely distributed proteins, that are specific for different groups of organisms at phylogenetic depths ranging from phylum to species levels. Due to their taxon specificity, these molecular markers provide novel and powerful means for evolutionary, systematic and diagnostic studies. Our work in this area has identified large numbers of such markers that are specific for different prokaryotic taxa enabling their identification and circumscription in molecular terms. My presentation will cover many examples showing the utilities of these markers for understanding prokaryotic phylogeny and systematics. In particular, the usefulness of these markers in clarifying the phylogeny and taxonomy of two important prokaryotic taxa i.e. the PVC clade of bacteria (consisting of Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae phylum) and the phylum Chloroflexi will be described.