Phylogenetic Analyses of homologous Amino Acid Sequences of Five Conserved Genes in Bacteria

Abstract

Using E. coli as a reference genome, the homologous amino acid sequences of five conserved genes, i.e., carB, dnaK, fusA, rpoB, and rpoC in E. coli, were obtained from other 24 bacterial genomes in GenBank and TIGR with GIST system. Phylogenetic analyses of these sequences were then performed using the neighbor-joining (NJ) method with PHYLIP. The unrooted phylogenetic trees based on the sequences of carB, fusA, rpoB, and rpoC show that Archaea and Eubacteria form two clearly separated clades and the six species within the Archaea can be distinguished. However, the relationship between Archaea and Eubacteria is not easy to be distinguished in the dnaK tree due to only one species of Archaea used in this study. The phylogenetic analyses of the five genes in Eubacteria were further conducted using the NJ, maximum parsimony (MP) and maximum likelihood (ML) methods with Methanothermobacterium thermoautrophicus as an outgroup. In general, the phylogenetic relationships of the bacteria inferred from the homologous amino acid sequences of the five conserved genes are reasonable, and GIST system can also be effectively used in future genome analysis.