Genome Sequences of Three Helicobacter pylori Strains Isolated from Atrophic Gastritis and Gastric Ulcer Patients in China

Abstract

Helicobacter pylori is a bacterial pathogen which can lead to several human gastric diseases. Here we describe the genome sequences of three strains isolated from atrophic gastritis and gastric ulcers patients in China. The data will permit genomic characterization of traits that may contribute to various gastric diseases.

GENOME ANNOUNCEMENT

Helicobacter pylori is widely known to be the primary cause of several severe diseases of the digestive system, such as gastritis, peptic ulceration, gastric adenocarcinoma, and MALT (mucus-associated lymphoid tissue) lymphoma (11, 16). It is also presumed to have coevolved with its human host, and it therefore reflects ancient human migrations. A number of phylogenetic studies have subdivided H. pylori into several distinct biogeographic populations, including hpAfrica1, hpAfrica2, hpEastAsia, and hpEurope. East Asian type (hpEastAsia) is further classified into at least three subtypes: East Asian (hspEAsia), Pacific (hspMaori), and native American (hspAmerind). The East Asia subtype (hspEAsia) may be related to the high incidence of gastric cancer in East Asia. Recent studies illustrate the East Asian group differ greatly from the European group in electron transfer and redox reactions, which implies a model of adaptive evolution and selection through proteome diversification and modulation of translational fidelity (5, 9, 10, 13).

Genome sizes among clinical isolates of H. pylori vary considerably, with some showing differences up to 25%. To date, there are over 30 completed genomes available on GenBank. Among these strains, there are in total six strains isolated from Japan and Korea, belonging to the hspEAsia group (1–4, 6, 7, 9, 12, 14, 15). Despite the fact that China is one of the countries with highest incidence of gastrointestinal diseases, few Chinese isolates have been sequenced so far (8).

In this study, we sequenced draft genomes of three strains isolated from Heilongjiang province, including isolates from two patients with atrophic gastritis (HLJ193 and HLJ256) and one patient with gastric ulcer (HLJ271). These strains were shown have a high genomic diversity compared to isolates involved in chronic superficial gastritis and gastric cancer in our previous studies (17). The strains were cultured on Columbia agar base supplemented with 5% sheep blood, and DNAs were extracted as previously described. For each strain, whole-genome sequencing was performed using Illumina HiSeq 2000 by generating paired-end libraries (500 bp and 2 kb) following the manufacturer's instructions. The read lengths were 90 bp and 50 bp for each library, from which more than 100 Mb of high-quality data were generated. Next, the paired-end reads from the two libraries were de novo assembled into scaffolds. Gene prediction was performed using Glimmer. The tRNA genes were searched for with tRNAScan-SE2. rRNA genes were searched for with RNAmmer3. Protein BLAST4 was run using the translated coding sequences as a query against the reference sequence (H. pylori strain 51). The best result for each BLAST search was imported as the gene annotation. Finally, we obtained 36 contigs, with a total length of 1,576,324 bp, and predicted 1,568 CDSs within the draft genome of strain HLJHP256. For strain HLJHP193, the contig number was 46, with a total length of 1,569,611 bp, and 1,596 CDSs were predicted. For strain HLJHP271, the contig number was 41, with a total length of 1,588,141 bp, and 1,633 CDSs were predicted. The average G+C content of the genome for each strain was 38.5%.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers ALJI00000000 (HLJ193), ALKA00000000 (HLJ256), and ALKB00000000 (HLJ271). The versions described in this paper are the first versions, ALJI00000000.1, ALKA00000000.1, and ALKB00000000.1.