| Comparative genomics reveals differences in gene order among species. In the genomes, genes are rearranged through inversion, transposition, translocation, and chromosome fission and fusion. Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. In this study, gene order data were used to resolve both shallow and deep relationships of prokaryotes and eukaryotes, including the genus Prochlorococcus, the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For instance, a previously unresolved node of MIT9211 and SS120 in Prochlorococcus is resolved. Both gene order phylogeny and sequence-based tree support two classes of methanogens, but the gene order phylogeny differs from the original classification of methanogens by placing Methanopyrales and Methanobacteriales together with Methanosarcinales rather than with Methanococcales. In addition, the gene order phylogeny supported Rodentia as an outgroup of the Primate-Carnivora-Perissodactyla clade. Our results suggest that the technique is useful in resolving the Tree of Life. Lastly, a comparative phylogenetic approach was designed to compare the gene families between Prochlorococcus and Synechococcus and we concluded that Prochlorococcus evolved towards genome reduction. |
