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

BMC Microbiology

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

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

LPS supergene combines sequencing data of 7 LPS genes (i.e. the 8LPS genes under study except for jhp0820)
HK supergene combines sequencing data of the 7 housekeeping genes studied by MLST
* Lengths of the phase variation mediating repeats have been standardized and major indels removed
^† Molecular distances were based on Kimura two-parameter estimates [28]
^‡ Synonymous substitutions (Ks) and non-synonymous substitutions (Ka) were determined using the methods of Nei and Gojobori [25]
^§ in strain JP9, two PCR products were obtained, showing that jhp0562 was present in two different loci

ISSN: 1471-2180