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Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease

Authors:
Rita Inés Armitano at Institute Infection Diseases" Carlos G. Malbran"
Rita Inés Armitano
  • Institute Infection Diseases" Carlos G. Malbran"
Gerardo Gabriel Zerbetto De Palma at Universidad de Buenos Aires
Gerardo Gabriel Zerbetto De Palma
Mario José Matteo
Mario José Matteo
Mario José Matteo
  • This person is not on ResearchGate, or hasn't claimed this research yet.
Santiago Revale at Alchemab Therapeutics
Santiago Revale
  • Alchemab Therapeutics
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Abstract

Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of gastric diseases in susceptible populations. Here we announce the draft genome sequences of strains HPARG8G and HPARG63. The data for both genome sequences provide insights regarding the diversity in gene content and rearrangement of the genomic islands commonly harbored by H. pylori.
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Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and
HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric
Ulcer Disease
Rita Inés Armitano,
a
Gerardo Zerbetto De Palma,
a
Mario José Matteo,
a
Santiago Revale,
b
Soledad Romero,
b
Germán Matías Traglia,
a
Mariana Catalano
a
Instituto de Microbiología y Parasitología Médica (IMPAM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones
Científicas y Tecnológicas, Buenos Aires, Argentina
a
; Instituto de Agrobiotecnología Rosario (INDEAR)-CONICET, CCT-CONICET, Rosario, Argentina
b
Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of gastric diseases in susceptible populations.
Here we announce the draft genome sequences of strains HPARG8G and HPARG63. The data for both genome sequences pro-
vide insights regarding the diversity in gene content and rearrangement of the genomic islands commonly harbored by H. pylori.
Received 7 August 2013 Accepted 9 August 2013 Published 5 September 2013
Citation Armitano RI, Zerbetto De Palma G, Matteo MJ, Revale S, Romero S, Traglia GM, Catalano M. 2013. Draft genome sequences of Helicobacter pylori strains HPARG63 and
HPARG8G, cultured from patients with chronic gastritis and gastric ulcer disease. Genome Announc. 1(5):e00700-13. doi:10.1128/genomeA.00700-13.
Copyright © 2013 Armitano et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Mariana Catalano, catalano@fmed.uba.ar.
Helicobacter pylori strain HPARG8G was isolated from a patient
with gastric ulcer disease and strain HPARG63 was recovered
from a patient with chronic gastritis. Here we report the draft genome
sequences of both strains. A total of 785,600 reads with an average
length of 435.02 nucleotides, corresponding to 33-fold coverage for
strain HPARG8G and 100-fold coverage for HPARG63, were ob-
tained with a 454 GS titanium pyrosequencer. De novo assembly
was done using 454 Newbler version 2.6, yielding 47 contigs for
HPARG8G and 34 contigs for HPARG63. The genomes were anno-
tated using the RAST server (1) and manually curated. Mauve (2) was
used to predict the order and orientation of the contigs, and Artemis
(3) was employed to glean details of the two genomes in comparison
with the closest overall neighbors predicted by RAST.
The Helicobacter pylori HPARG8G genome sequence com-
prises 1,596,552 bp and 1,568 coding sequences (RAST) as well as
36 tRNAs and 2 rRNAs. The average G⫹C content was 38.98%.
The HPARG63 strain genome sequence contains approximately
1,668,716 bp and 1,623 coding sequences and also has 36 tRNAs
and 2 rRNAs, with an average G⫹C content of 38.79%. The H. py-
lori P12 strain was predicted by RAST as one of the closest overall
neighbors of HPARG8G and HPARG63. Both genomes displayed
a conserved repertoire of housekeeping genes corresponding to
various metabolic pathways. The two genomes each showed a
complete cag pathogenicity island (cag PAI), with the complex
rearrangement in the region delimited by dapB and murI genes
described in the Mongolian gerbil-colonizing strain H. pylori B8
(4). In HPARG8G and HPARG63, the cagA gene was located
12,726 bp and 11,982 bp downstream from the cagB-cag1 region,
respectively. Consequently, the complete cag PAI gene order
might not be as highly conserved as had been proposed previously
(5). The HPARG63 strain contained two transposon of plasticity
zone (TnPZ) elements (6). TnPZ type 1b lacked the genes
HPP12_455 through HPP12_457 found in the same element in
strain P12; the HPP12_459 through HPP12_461 genes from the
type IV secretion system TFS4 were also absent (7). In both strains,
this TnPZ was inserted in a pseudogene similar to hp0464 of strain
26695 (7). In addition, the HPARG63 element harbored the
virD2-virD4,virB11-virB9, and topA genes with the highest ho-
mology to genes of other H. pylori strains. The second element was
a TnPZ type 2 remnant located in an unusual chromosomal inser-
tion site, containing few type IV secretion system TFS3 genes. The
strain HPARG8G carried only xerD,jhp0959,jhp0949, and
jhp0948 genes from the TnPZ type 1b left end (6) and hp0444,
hp0445, and hp0446 genes from the TFS4, inserted in a methyl-
transferase type II system. Our findings support the hypothesis
that although the TnPZs are genomic elements transferable as a
whole, they often contain only subsets of the genes present on the
complete islands (6,7).
Nucleotide sequence accession numbers. The first versions of
the HPARG8G and HPARG63 sequences are accessible at the
European Nucleotide Archive (http://www.ebi.ac.uk/ena/) under
accession numbers CBKZ010000001 through CBKZ010000047
and CBKY010000001 through CBKY010000034.
ACKNOWLEDGMENTS
This project was supported by grants BID 1728 OC-AR-PICT 2010-1492
provided by the Agencia Nacional de Promoción Científica y Tecnológica
and M064 from the Universidad de Buenos Aires (UBACyT-2010-2012).
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Armitano et al.
Genome Announcements2genomea.asm.org September/October 2013 Volume 1 Issue 5 e00700-13
Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disea
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... These populations generally correspond to their geographical origins. Up to date, hundreds of strains have been sequenced or being sequenced [9][10][11][12] . The purpose of this review is to compare the genomic differences of H. pylori from different populations, and discuss their implications in the geographical variation of the prevalence of the infection. ...
... To explore the genomic differences between H. pylori strains, we have determined the genome sequence of H. pylori strain D33 isolated from a Chinese patient with gastric cancer. Whole-genome sequencing was performed as described previously [9,10] . Briefly, the raw reads were trimmed and filtered, yielding a total of 2364383 reads with an average length of 260 nucleotides. ...
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Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements
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Reordering contigs of draft genomes using the Mauve Aligner
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WebACT - An online companion for the Artemis Comparison Tool
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The RAST server: rapid annotations using subsystems technology
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  • BMC GENOMICS
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A global overview of the genetic and functional diversity in the Helicobacter pylori cag pathogenicity island
  • Jan 2010
  • PLOS GENET
  • 1001069
  • P Olbermann
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  • S Suerbaum
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