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Codon-pair context is species specific.A) Individual codon-pair context maps built for various genomes followed phylogeny indicating that codon-pair context is species specific. For instance, the human ORFeome map is more similar to that of chimpanzee (Pan troglodytes) than to the mouse (Mus musculus) map. B) This result was confirmed using differential display maps (DDM) that subtract two codon-pair context maps. For example, H. sapiens–M. musculus (H.s vs M.m); H. sapiens–P. troglodytes (H.s vs P.t). In these differential display maps major codon-pair context differences (above 15) are shown in light blue and darker maps correspond to species with more similar codon-pair context biases. In the present example, the maps of H.s vs M.m and H.s vs P.t have 6% and 1% of blue cells, respectively. C and D) The same phylogenetical relationship could be detected for bacterial ORFeomes, as exemplified for Escherichia coli, Bacillus cereus and Salmonella typhi. The DDM built with these species have 55% (E.c vs B.c) and 20% (E.c vs S.t) of blue cells. E) Finally, the phylogenetical relationship was maintained when the above species were clustered according to the similarities of the codon-pair context maps. The yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe were added to include an intermediate group of lower eukaryotes in the tree. Adjusted residuals are colored in the maps according to the color scale shown, so that green cells correspond to preferred and red cells to rejected contexts.

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