Phylogenetic signals in DNA composition: limitations and prospects.

The concept of genome signature allows sequence comparisons without alignment. It relies on the premise that oligonucleotide compositions of DNA segments from the same or closely related genomes tend to be more similar than those from distantly related genomes. This concept has been used in detection of lateral gene transfer, phylogenetic classification of metagenome sequences (binning), and in studies of evolution of viruses and plasmids. The goal of this work is to explore limitations of genome signature in phylogenetic classification of DNA sequences and to identify formal representations of genome signature that expose best the phylogenetic relationships among prokaryotes. We found that genome signatures that best represent phylogenetic relationships are those normalized to factor out differences in G + C content and utilizing the standard A-C-G-T alphabet or the degenerate R-Y (purine-pyrimidine) alphabet. The main limitation of all genome signature representations tested is lack of divergence among some distantly related species. "Crowding" of the genome signature space and absence of molecular clock likely contribute to this phenomenon. We introduce "periodicity signatures"--formal representations of periodic sequence patterns related to DNA curvature--which can discriminate between bacterial and archaeal DNA sequences. Interestingly, archaea of the order Halobacteriaceae have periodic signatures similar to bacteria, possibly due to their early divergence from other archaea, extensive lateral gene transfer, or due to their adaptation to high salt environments. Our results have practical implications for development and application of genome signature-based methods for analysis and classification of DNA sequences.