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Table 6 Genes diverged between East Asian and European H. pylori

From: Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pyloriEast Asian genomes

Gene Description Representative of the gene family(a,b,c) Distance d a (d) Distance d b (e) d b zone Reference
hpaA-2 HpaA paralog HP0492(f) 0.1608 0.0253 3 [68]
cagA Cag pathogenicity island protein HP0547(f) 0.1009 0.0285 3 [11]
  Bacterial SH3 domain HP1250 0.0901 0.0615 3  
futA, futB α-(1,3)-fucosyltransferase HP0379, HP0651 0.0553 0.0436 3 [15]
sotB Sugar efflux transporter HP1185 0.0441 0.0095 2  
vacA Vacuolating cytotoxin A HP0887 0.0420 0.0137 2 [67]
miaA tRNA delta(2)-isopentenylpyrophosphate transferase mHP1415 0.0373 0.0241 3 [64, 144]
  Hypothetical protein HPAG1_0619 0.0366 0.0540 3  
hcpD Cysteine-rich protein, SLR (Sel1-like repeat) protein HP0160 0.0363 0.0323 3 [16]
yajC Preprotein translocase subunit YajC HP1551 0.0353 0.0268 3 [81]
agt β-1,3-N-acetyl-glucosaminyl transferase HP1105 0.0338 0.0228 2  
rnhB Ribonuclease HII mHP1323(f) 0.0337 0.0398 3 [103, 104]
fliK Flagellar hook length control HP0906 0.0328 0.0382 3 [85]
homC Putative outer membrane protein HP0373 0.0325 0.1207 3  
hopJ,hopK Outer membrane protein HP0477, HP0923 0.0313 0.0357 3 [27]
frxA NAD(P)H-flavin oxidoreductase HP0642 0.0306 0.0212 2 [120]
secG Preprotein translocase subunit SecG mHP1255 0.0300 0.0226 2 [80]
  Hypothetical protein HP0384 0.0296 0.0302 3  
tipα Tumor necrosis factor alpha-inducing protein HP0596 0.0293 0.0145 2 [66]
hydE Membrane-bound, nickel containing, hydrogen uptake hydrogenase HP0635 0.0288 0.0252 3 [92]
tilS tRNA(Ile) lysidine synthase HP0728 0.0286 0.0193 2 [96, 97]
comH Periplasmic competence protein HP1527 0.0285 0.0194 2 [82]
def Peptide deformylase HP0793 0.0285 0.0065 2 [98]
vacA-4 Putative vacuolating cytotoxin-like protein HP0922 0.0284 0.0222 2  
hypD Hydrogenase expression/formation protein HP0898 0.0284 0.0169 2 [91, 145, 146]
addA Helicase HP1553 0.0283 0.0308 3 [100]
hsdR Type I restriction enzyme, R protein mHP1402 0.0282 0.0245 3  
  Hypothetical protein mHP0174 0.0268 0.0203 2  
oipA,oipA-2 Outer membrane protein OipA HP0638 0.0267 0.0097 2 [70]
prmA Ribosomal protein L11 methyltransferase HP1068 0.0261 0.0118 2 [99]
maf Maf family (motility accessory family of flagellin-associated proteins) homolog HP0465 0.0259 0.0214 2 [86]
  Hypothetical protein HP0097 0.0257 0.0207 2  
  Hypothetical protein HP1143 0.0254 0.0146 2  
cvpA Membrane protein required for colicin V production and secretion mHP0181 0.0252 0.0169 2 [83]
pgl 6-phosphogluconolactonase HP1102 0.0250 0.0130 2  
horI Outer membrane protein Horl HP1113 0.0248 0.0348 3  
fixQ cbb3-type cytochrome c oxidase subunit Q mHP0146 0.0248 0.0023 1  
  Hypothetical protein HP0150 0.0248 0.0154 2  
cheY Chemotaxis effector HP1067 0.0248 0.0014 1 [84]
fliT Flagellar chaperone HP0754 0.0245 0.0138 2 [84]
ftsA Cell division protein HP0978 0.0244 0.0071 2 [105, 106]
rnhA Ribonuclease H HP0661 0.0243 0.0217 2 [103, 104]
ilvE Branched-chain amino acid aminotransferase HP1468 0.0239 0.0136 2  
fixS Cation transport subunit for cbb3-type oxidase HP1163 0.0237 0.0250 3 [87]
nuoF NADH-ubiquinone oxidoreductase chain F HP1265 0.0236 0.0202 2  
  Putative thiol:disulfide interchange protein HP0861 0.0234 0.0185 2  
  Hypothetical protein HP0806 0.0233 0.0233 3  
  1. (a) m, different assignment of start codon from the RefSeq entry in the GenBank database
  2. (b) All paralogous genes in each orthologous group are counted.
  3. (c) Assignments to gene families are in Additional file 5 (= Table S4).
  4. (d) Distance between the last common ancestor of hspEAsia and the last common ancestor of hpEurope.
  5. (e) Average of distances between the last common ancestor of hspEAsia and each hspEAsia strain.
  6. (f) A homolog in the draft genome sequence of another East Asian strain 98-10 has been reported to be diverged from four Western strains [143]. The other genes listed as diverged in 98-10 [143], HP0806, HP0061, HP1524, HP0519 and HP1322, did not meet the criteria of this study. HP0806 was below the d a threshold; for the others, the hspEAsia genes did not form a separate sub tree from hpEurope.