Uncovering Rate Variation of Lateral Gene Transfer during Bacterial Genome Evolution:

Supplementary Materials


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 DescriptionInformational?
argS JTranslation Yes
gltX JTranslation Yes
hisS JTranslation Yes
infB JTranslation Yes
ksgA JTranslation Yes
lysS JTranslation Yes
metG J, RTranslation, General function prediction only Yes
pheS JTranslation Yes
proS JTranslation Yes
serS JTranslation Yes
ychF JTranslation Yes
nusA KTranscription Yes
nusG KTranscription Yes
rpoA KTranscription Yes
gcp OPosttranslational modification, protein turnover No
secY UIntracellular trafficking and secretionNo

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
Rhodopseudomonas1140 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

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