Phylogenetic Marker Identification in Bacteria and Archaea

Bacterial and archaeal genomes from the IMG database were selected for phylogenetic marker identification. Only genomes that were complete were included. We started our marker identification process at 15 different taxonomic levels: the domain Archaea; the phyla Actinobacteria, Bacteroides, Chlamydiae, Chloroflexi, Cyanobacteria, Firmicutes, Spirochetes, Deinococcus-Thermus and Thermotogae; the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria. Genomes that have undergone major genome reductions, such as those of Mycoplasma [45] (link), [46] (link) and gammaproteobacteria endosymbionts [47] (link), [48] (link), were not included in this study. Only one strain of the same species within Gammaproteobacteria was selected if other strains did not contribute to the phylogenetic diversity (PD) in the phylogenetic tree of bacteria.
A ssu-rRNA phylogenetic tree was built for all the genomes in the selection. Alignments of ssu-rRNAs were extracted from the greengenes database[49] (link). Fasttree was used for ssu-rRNA tree building[50] (link).