Overlapping genes as rare genomic markers: the phylogeny of gamma-Proteobacteria as a case study.

Phylogenies can be constructed in many ways, including using shared complex characters known as rare genomic changes (RGCs), such as insertions and deletions (indels), retroposon integrations and intron positions. Here, we demonstrate that distance-based phylogenies, which were determined by shared overlapping genes from 13 completely sequenced gamma-Proteobacteria genomes, are consistent with phylogenies based on 16S rRNAs and other robust markers. These findings suggest that overlapping genes could provide interesting additional insights into the phylogenomics of completely sequenced microbial genomes.