Bacterial whole genome phylogeny using proteome comparison and optimal reversal distance

Traditional phylogenetic tree reconstruction is based on point mutations of a single gene. This approach is hardly suitable for genomes whose genes are almost identical and hardly captures evolutionary scenarios. To reconstruct a more conclusive phylogenetic tree of bacterial genome, all currently available complete bacterial genomic sequences were downloaded from the National Center for Biotechnology Information (NCBI). Each individual proteome was blasted against the collection and provided a number of homologous genes shared with others. Moreover, the syntenies of each two genomes can be considered as two signed permutations. One permutation can be rearranged into another in finite steps, called reversal distance. These two measures were combined and yield a phylogenetic tree that is highly consistent with the bacterial taxonomy.