Table 1.
Complete Genomes Used in the Work Arranged as They Appear in the Figures
| Kingdom | Taxonomical adscription | Species | ||
| Rank 1 | Rank 2 | Rank 3 | ||
| Bacteria | Proteobacteria | Gamma | Enterobacteria | Escherichia coli K12 Escherichia coli O157 Salmonella typhimurium LT2 Salmonella typhi Yersinia pestis |
| Vibronaceae | Vibrio cholerae | |||
| Enterobacteria | Buchnera aphidicola | |||
| Pasteurellaceae | Haemophilus influenzae Pasteurella multicocida | |||
| Pseudomonadaceae | Pseudomonas aeruginosa | |||
| Xantomonas | Xilella fastidiosa | |||
| Alpha | Rhizobiaceae | Rhizobium meliloti Rhizobium loti Agrobacterium tumefaciens | ||
| Caulobacter | Caulobacter crescentus | |||
| Rickettsiales | Rickettsia prowazekii Rickettsia conorii | |||
| Beta | Neisseriaceae | Neisseria meningitidis MC58 Neisseria meningitidis Z2491 | ||
| Epsilon | Helicobacter | Helicobacter pylori J99 Helicobacter pylori | ||
| Campylobacter | Campylobacter jejuni | |||
| Firmicutes | Bacillus/Clostridium | Bacillus/Staphylococcus | Bacillus subtilis Bacillus halodurans Staphylococcus aureus Staphylococcus aureus Mu50 Listeria innocua Listeria monocytogenes | |
| Streptococcaceae | Streptococcus pyogenes Streptococcus pneumoniae Lactococcus lactis | |||
| Clostridia | Clostridium acetobitylicum | |||
| Mollicutes | Ureaplasma parvum Mycoplasma pulmonis Mycoplasma pneumoniae Mycoplasma genitalum | |||
| Actinobacteria | Actinobacteridae | Mycobacterium tuberculosis Mycobacterium leprae | ||
| Thermus | Deinococcus | Deinococcus radiodurans | ||
| Cyanobacteria | Chroococcales | Synechocystis | Synechocystis sp | |
| Aquificales | Aquificaceae | Aquifex | Aquifex aeolicus | |
| Thermotogales | Thermotoga | Thermotoga maritima | ||
| Spirochaetales | Spirochaetaceae | Borrellia | Borrellia burgdorferi | |
| Treponema | Treponema pallidum | |||
| Chlamydiales | Chlamydiaceae | Chlamydia pneumoniae Chlamydia muridarum Chlamydia trachomatis | ||
| Archaea | Euryarchaeota | Halobacteriales | Halobacteriaceae | Halobacterium sp |
| Thermococcales | Thermococcaceae | Pyrococcus horikoshii Pyrococcus abysii | ||
| Thermoplasmales | Thermoplasmaceae | Thermoplasma volcanicum Thermoplasma acidophilum | ||
| Archaeoglobales | Archaeoglobaceae | Archaeglobus fulgidus | ||
| Methanococcales | Methanococcaceae | Methanococcus janascii | ||
| Methanobacteriales | Methanobacteriaceae | Methanobacteria thermoautotrophicum | ||
| Crenarchaeota | Desulfurococcales | Desulfurococcaceae | Aeropyrum pernix | |
| Sulfolobales | Sulfolobaceae | Sulfolobus solfataricus Sulfolobus tokodaii | ||
References for the genomes can be found in the Web page of genomes at EBI (http://www.ebi.ac.uk/genomes/index.html)