Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA

Our basic observation is that each genome has a characteristic "signature" defined as the ratios between the observed dinucleotide frequencies and the frequencies expected if neighbors were chosen at random (dinucleotide rela tive abundances). The remarkable fact is that the signature is relatively c onstant throughout the genome; i.e., the patterns and levels of dinucleotid e relative abundances of every 50-kb segment of the genome are about the sa me. Comparison of the signatures of different genomes provides a measure of similarity which has the advantage that it looks at all the DNA of an orga nism and does not depend on the ability to align homologous sequences of sp ecific genes. Genome signature comparisons show that plasmids, both special ized and broad-range, and their hosts have substantially compatible (simila r) genome signatures. Mammalian mitochondrial (Mt) genomes are very similar , and animal and fungal Mt are generally moderately similar, but they diver ge significantly from plant and protist Mt sets. Moreover, Mt genome signat ure differences between species parallel the corresponding nuclear genome s ignature differences, despite large differences between Mt and host nuclear signatures. In signature terms, we find that the archaea are not a coheren t clade, For example, Sulfolobus and Halobacterium are extremely divergent. There is no consistent pattern of signature differences among thermophiles . More generally, grouping prokaryotes by environmental criteria (e.g., hab itat propensities, osmolarity tolerance, chemical conditions) reveals no co rrelations in genome signature.