Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8

Farnbacher M, Jahns T, Willrodt D, Daniel R, Haas R, Goesmann A, Kurtz S, Rieder G (2010)
BMC Genomics 11(1): 335.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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urn:nbn:de:0070-pub-17855793
Autor*in
Farnbacher, Max; Jahns, Thomas; Willrodt, Dirk; Daniel, Rolf; Haas, Rainer; Goesmann, AlexanderUniBi ; Kurtz, Stefan; Rieder, Gabriele
Einrichtung
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Technische Fakultät > Computational Genomics
Abstract / Bemerkung
Background: The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128. Results: The complete genome of H. pylori B8 was manually curated gene by gene, to assign as much function as possible. It consists of a circular chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp carrying nine putative genes. The chromosome contains 1,711 coding sequences, 293 of which are strain-specific, coding mainly for hypothetical proteins, and a large plasticity zone containing a putative type-IV-secretion system and coding sequences with unknown function. The cag-pathogenicity island is rearranged such that the cagA-gene is located 13,730 bp downstream of the inverted gene cluster cagB-cag1. Directly adjacent to the cagA-gene, there are four hypothetical genes and one variable gene with a different codon usage compared to the rest of the H. pylori B8-genome. This indicates that these coding sequences might be acquired via horizontal gene transfer. The genome comparison of strain B8 to its parental strain B128 delivers 425 unique B8-proteins. Due to the fact that strain B128 was not fully sequenced and only automatically annotated, only 12 of these proteins are definitive singletons that might have been acquired during the gerbil-adaptation process of strain B128. Conclusion Our sequence data and its analysis provide new insight into the high genetic diversity of H. pylori-strains. We have shown that the gerbil-adapted strain B8 has the potential to build, possibly by a high rate of mutation and recombination, a dynamic pool of genetic variants (e.g. fragmented genes and repetitive regions) required for the adaptation-processes. We hypothesize that these variants are essential for the colonization and persistence of strain B8 in the gerbil stomach during inflammation.
Erscheinungsjahr
2010
Zeitschriftentitel
BMC Genomics
Band
11
Ausgabe
1
Art.-Nr.
335
ISSN
1471-2164
Page URI
https://pub.uni-bielefeld.de/record/1785579

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Farnbacher M, Jahns T, Willrodt D, et al. Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics. 2010;11(1): 335.
Farnbacher, M., Jahns, T., Willrodt, D., Daniel, R., Haas, R., Goesmann, A., Kurtz, S., et al. (2010). Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics, 11(1), 335. https://doi.org/10.1186/1471-2164-11-335
Farnbacher, Max, Jahns, Thomas, Willrodt, Dirk, Daniel, Rolf, Haas, Rainer, Goesmann, Alexander, Kurtz, Stefan, and Rieder, Gabriele. 2010. “Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8”. BMC Genomics 11 (1): 335.
Farnbacher, M., Jahns, T., Willrodt, D., Daniel, R., Haas, R., Goesmann, A., Kurtz, S., and Rieder, G. (2010). Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics 11:335.
Farnbacher, M., et al., 2010. Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics, 11(1): 335.
M. Farnbacher, et al., “Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8”, BMC Genomics, vol. 11, 2010, : 335.
Farnbacher, M., Jahns, T., Willrodt, D., Daniel, R., Haas, R., Goesmann, A., Kurtz, S., Rieder, G.: Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics. 11, : 335 (2010).
Farnbacher, Max, Jahns, Thomas, Willrodt, Dirk, Daniel, Rolf, Haas, Rainer, Goesmann, Alexander, Kurtz, Stefan, and Rieder, Gabriele. “Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8”. BMC Genomics 11.1 (2010): 335.
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Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J., Bioinformatics 21(16), 2005
PMID: 15976072
Laboratory of Phil Green
AUTHOR UNKNOWN, 0
The Staden package, 1998.
Staden R, Beal KF, Bonfield JK., Methods Mol. Biol. 132(), 2000
PMID: 10547834
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol. 5(2), 2004
PMID: 14759262
OSLay: optimal syntenic layout of unfinished assemblies.
Richter DC, Schuster SC, Huson DH., Bioinformatics 23(13), 2007
PMID: 17463020
The Vmatch large scale sequence analysis software
AUTHOR UNKNOWN, 0
Genome update: DNA repeats in bacterial genomes.
Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF., Microbiology (Reading, Engl.) 150(Pt 11), 2004
PMID: 15528640
Correspondence Analysis of Codon Usage
AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 2009
AnnotationSketch: a genome annotation drawing library.
Steinbiss S, Gremme G, Scharfer C, Mader M, Kurtz S., Bioinformatics 25(4), 2008
PMID: 19106120
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