The Japanese and Korean strains were not separated into two clusters. PeCan4 appeared diverged from the other four hspAmerind strains JQEZ5 as expected from the result of the phylogenetic analysis based on the 7 genes described above. SJM180 appeared diverged from the other hpEurope strains in the well-defined core gene-based tree. Figure 1 Phylogenetic

tree of 20 H. pylori strains based on their well-defined core genes. Well-defined core OGs were used for neighbor-joining method (see Methods). Numbers indicate bootstrap values. Scale bar indicates substitutions per nucleic acid residue (change/nucleotide site). The assignment of population/subselleckchem population was based on a phylogenetic tree constructed from the concatenated alignment of fragments of seven genes used in the H. pylori MLST database (atpA, efp, mutY, ppa, trpC, ureI and yphC) [18]. Classification of population/subpopulation was as described [10, 19]. Phylogenetic profiling to identify gene

contents EVP4593 order of hspEAsia To thoroughly characterize the gene contents specific to the Japanese/Korean (hspEAsia) strains, we conducted phylogenetic profile analysis using the DomClust program [24]. This analysis determines the presence or absence of a domain, rather than a gene, and allows detection of split genes, partially deleted genes and partially duplicated genes (detailed in Methods). Their features will be explained in the

next five sections. Differences in outer membrane proteins and related proteins in the number of loci of gene families and in alleles at each locus One of the emerging almost features of the East Asian (hspEAsia) strains is the change in the number of loci of some of the outer membrane protein (OMP) families. We detected five OMP genes (gene families; oipA, hopMN, sabAB, babABC and vacA-2) with the number of loci different between the hspEAsia and hpEurope strains (Table 2). In all but one gene family, the difference in the number of locus was the result of gene decay in the East Asian (hspEAsia) strains. Table 2 Characteristic gene contents of East Asian (hspEAsia) H.