Component Distance Method To Build Phylogenetic Tree Based On Two Groups Of Proteins In Prokaryotes

Carl Woese firstly aligned the small subunit ribosomal RNA (SSU rRNA) sequences to infer phylogenetic relations of procaryotes in 1970s. Now many biologists still regard SSU rRNA tree as the standard tree of life. However, lots of new motheds inferring phylogenetic relations appeared with all kinds of completion of sequencing of procaryote genomes. Recently, our group have developed a K-string composition distance method. Originally, we have applied to whole proteome resulting in better evolutionary tree. It's the same as the trees that we used all ribosomal proteins or the set of aminoacyl tRNA synmetases for each species to construct. The latter group has been known to yield inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea, 105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, edition of the Bergey's Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa. Comparison with the trees based on SSU rRNA, or proteome, or genome, or RDP Backbone tree, not only shows proofs, but also complements some details.