The online version of this article (doi:10.1186/1757-4749-6-5) contains supplementary material, which is available to authorized users.
The authors declare that they have no competing interests.
YY performed the bioinformatics analysis and wrote the manuscript; MZ and LH were responsible for bacteria isolation and identification; LL, XH and YZ performed genomic sequencing; JZ and PN designed the study and provided financial support for this work. All authors read and approved the final manuscript.
Helicobacter pylori is well known for its relationship with the occurrence of several severe gastric diseases. The mechanisms of pathogenesis triggered by H. pylori are less well known. In this study, we report the genome sequence and genomic characterizations of H. pylori strain HLJ039 that was isolated from a patient with gastric cancer in the Chinese province of Heilongjiang, where there is a high incidence of gastric cancer. To investigate potential genomic features that may be involved in pathogenesis of carcinoma, the genome was compared to three previously sequenced genomes in this area.
We obtained 42 contigs with a total length of 1,611,192 bp and predicted 1,687 coding sequences. Compared to strains isolated from gastritis and ulcers in this area, 10 different regions were identified as being unique for HLJ039; they mainly encoded type II restriction-modification enzyme, type II m6A methylase, DNA-cytosine methyltransferase, DNA methylase, and hypothetical proteins. A unique 547-bp fragment sharing 93% identity with a hypothetical protein of Helicobacter cinaedi ATCC BAA-847 was not present in any other previous H. pylori strains. Phylogenetic analysis based on core genome single nucleotide polymorphisms shows that HLJ039 is defined as hspEAsia subgroup, which belongs to the hpEastAsia group.
DNA methylations, variations of the genomic regions involved in restriction and modification systems, are the “hot” regions that may be related to the mechanism of H. pylori-induced gastric cancer. The genome sequence will provide useful information for the deep mining of potential mechanisms related to East Asian gastric cancer.
Additional file 1:General information for the publicly available genomes.(DOC 60 KB)13099_2014_126_MOESM1_ESM.doc
Additional file 2:Assembly information for HLJ039.(DOC 27 KB)13099_2014_126_MOESM2_ESM.doc
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- Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China
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