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Table 2 Diversity within H. pylori LPS genes and housekeeping genes under study

From: Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori

gene number of sequences compared length compared (nt)* nucleotide identity (%) genetic distances Ks Ka Ka/Ks
LPS genes        
LPS supergene 23 × 7 7335 75.62 ± 14.62 0.07 ± 0.02 0.27 ± 0.08 0.05 ± 0.01 0.18 ± 0.02
   HP0651 23 1065 88.49 ± 3.15 0.12 ± 0.03 0.49 ± 0.16 0.07 ± 0.02 0.15 ± 0.03
   HP0379 22 1065 89.15 ± 3.22 0.11 ± 0.03 0.44 ± 0.15 0.07 ± 0.02 0.15 ± 0.03
   HP0093 23 873 94.64 ± 1.93 0.05 ± 0.02 0.20 ± 0.08 0.02 ± 0.01 0.12 ± 0.03
   HP0619 17 1119 91.29 ± 2.68 0.09 ± 0.03 0.29 ± 0.10 0.05 ± 0.02 0.20 ± 0.06
   jhp0562 19 + 1§ 999 92.20 ± 3.45 0.08 ± 0.03 0.26 ± 0.11 0.05 ± 0.03 0.19 ± 0.07
   HP0208 20 1128 92.40 ± 2.27 0.08 ± 0.02 0.24 ± 0.08 0.05 ± 0.01 0.21 ± 0.04
   jhp0820 11 1110 90.83 ± 8.33 0.10 ± 0.10 0.27 ± 0.24 0.10 ± 0.13 0.37 ± 0.15
   HP0217 21 1086 94.40 ± 2.13 0.05 ± 0.02 0.19 ± 0.08 0.03 ± 0.01 0.18 ± 0.06
HK genes        
HK supergene 23 3402 95.31 ± 1.47 0.05 ± 0.02 0.21 ± 0.07 0.01 ± 0.01 0.06 ± 0.01
  1. LPS supergene combines sequencing data of 7 LPS genes (i.e. the 8LPS genes under study except for jhp0820)
  2. HK supergene combines sequencing data of the 7 housekeeping genes studied by MLST
  3. * Lengths of the phase variation mediating repeats have been standardized and major indels removed
  4. Molecular distances were based on Kimura two-parameter estimates [28]
  5. Synonymous substitutions (Ks) and non-synonymous substitutions (Ka) were determined using the methods of Nei and Gojobori [25]
  6. § in strain JP9, two PCR products were obtained, showing that jhp0562 was present in two different loci