1) The best supported tree of each group is given Here.
2) The genes used for phylogeny construction in each group are listed below.
Bacillus | gcP, gltX, infB, nusA, pheS, rpoA, ychF |
Brucella | argS, ksgA, metG, nusA, nusG, pheS, proS, rpoA, secY, serS |
Burkholderia | argS, infB, ksgA, metG, nusA, nusG, pheS, proS, rpoA, secY, serS |
Candidatus | argS, gcp, gltX, ksgA, pheS, rpoA, secY, serS, ychF |
Chlamydophila | argS, gcp, ychF, lysS, gltX, hisS, infB, kgsA, metG, nusA, nusG, pheS, proS, rpoA, secY, serS |
Clostridium | argS, gcp, ychF, gltX, metG, nusA, nusG, pheS, proS, rpoA, secY |
Corynebacterium | argS, gltX, ksgA, ychF, nusA, gltS, hisS, infB, lysS, metS, nusG, pheS, proS, rpoA, secY, serS |
Ehrlichia | argS, gcp, hisS, infB, ksgA, lysS, metG, nusA, nusG, pheS, proS, rpoA, secY, serS, ychF |
Escherichia | argS, gltX, hisS, infB, ksgA, metG, nusA, nusG, pheS, prlA, proS, rpoA, serS, ychF |
Helicobacter | argS, gcp, hisS, infB, ksgA, lysS, metS, nusA, nusG, pheS, proS, rpoA, secY, serS |
Lactobacillus | argS, gcp, gltX, hisS, infB, ksgA, metS, nusA, nusG, pheS, pheT, proS, rpoA |
Mycobacterium | gcp, gltS, hisS, infB, ksgA, lysS, lysX, nusA, nusG, pheS, rpoA, secY, serS |
Mycoplasma | argS, gltX, infB, ksgA, pheS, proS, secY, serS, ychF |
Prochlorococcus | argS, gltX, hisS, hisZ, infB, ksgA, lysS, metG, nusG, pheS, proS, rpoA, secY, serS |
Pseudomonas | argS, gcp, gltX, hisS, infB, ksgA, lysS, metG, nusA, nusG, pheS, proS, rpoA, secY, serS, ychF |
Rhodopseudomonas | argS, gcp, gltX, infB, ksgA, lysS, nusA, nusG, pheS, proS, rpoA, secY, serS |
Rickettsia | argS, gcp, hisS, infB, ksgA, lysS, metS, nusA, nusG, pheS, proS, rpoA, secY, serS, ychF |
Salmonella | argS, gcp, gltX, hisS, infB, ksgA, lysS, metG, nusA, nusG, pheS, proS, rpoA, secY, serS, ychF |
Shigella | argS, gltX, hisS, infB, ksgA, metG, nusA, nusG, pheS, proS, rpoA, serS, ychF |
Staphylococcus | argS, gltX, hisS, infB, ksgA, metS, nusA, nusG, pheS, proS, rpoA, serS, ychF |
Streptococcus | argS, hisS, infB, ksgA, metS, nusA, nusG, pheS, proS, rpoA, serS, ychF |
Synechococcus | argS, gcp, gltX, hisS, hisZ, ksgA, lysS, metG, nusA, nusG, pheS, proS, rpoA, secY, serS |
Vibrio | argS, gltX, hisS, hisS, ksgA, lysS, metS, nusA, pheS, proS, rpoA, secY, serS |
Xanthomonas | ksgA, lysS, nusG, proS, rpoA |
Yersinia | argS, gcp, gltX, hisS, ksgA, lysS, metS, nusA, nusG, pheS, proS, rpoA, secY, serS |
3) COGs functional categories of the genes above.
Gene | COGs | Description | Informational? |
argS | J | Translation | Yes |
gltX | J | Translation | Yes |
hisS | J | Translation | Yes |
infB | J | Translation | Yes |
ksgA | J | Translation | Yes |
lysS | J | Translation | Yes |
metG | J, R | Translation, General function prediction only | Yes |
pheS | J | Translation | Yes |
proS | J | Translation | Yes |
serS | J | Translation | Yes |
ychF | J | Translation | Yes |
nusA | K | Transcription | Yes |
nusG | K | Transcription | Yes |
rpoA | K | Transcription | Yes |
gcp | O | Posttranslational modification, protein turnover | No |
secY | U | Intracellular trafficking and secretion | No |
4) Phylogeny was also constructed using all common genes that do not have paralogs. The phylogeny of each group was compared with the one using the genes in 2). If (and only if) there is incongruence, all genes present in at least 4 genomes were used to construct a supertree. To view all the phylogenies, click Here.
Group | Number of genes | Topology comparison | Number of genes used for supertree |
Bacillus | 386 | Different | 3407 |
Brucella | 591 | Different | 591 |
Burkholderia | 634 | Different | 2126 |
Candidatus | 134 | Same | - |
Chlamydophila | 637 | Same | - |
Clostridium | 309 | Different | 1141 |
Corynebacterium | 578 | Same | - |
Ehrlichia | 517 | Same | - |
Escherichia | 1700 | Different | 2980 |
Helicobacter | 584 | Same | - |
Lactobacillus | 339 | Different | 923 |
Mycobacterium | 607 | Same | - |
Mycoplasma | 79 | Different | 433 |
Prochlorococcus | 617 | Same | - |
Pseudomonas | 579 | Different | 3102 |
Rhodopseudomonas | 1140 | Same | - |
Rickettsia | 266 | Same | - |
Salmonella | 1580 | Same | - |
Shigella | 1476 | Different | 2608 |
Staphylococcus | 565 | Different | 1902 |
Streptococcus | 400 | Different | 1690 |
Synechococcus | 630 | Same | - |
Vibrio | 971 | Different | 1780 |
Xanthomonas | 321 | Same | - |
Yersinia | 1260 | Different | 2752 |