APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange

Oliver Bezuidt, Kingdom Mncube, Oleg N. Reva

Abstract

With more sequences of complete bacterial genomes getting public availability the approaches of genome comparison by frequencies of oligonucleotides (k-mers) known also as the genome linguistics are becoming popular and practical to resolve problems which can not be tackled by the traditional sequence comparison tools. In this work we present several innovative approaches based on k-mer statistics for detection of inserts of genomic islands and tracing down the ontological links and origins of mobile genetic elements. 637 bacterial genomes were analyzed by SeqWord Sniffer program that has detected 2,622 putative genomic islands. These genomic islands were clustered by DNA compositional similarity. A stratigraphic analysis was introduced that allows distinguishing between new and old genomic inserts. A method of reconstruction of donor-recipient relations between micro-organisms was proposed. The strain E. coli TY-2,482 isolated from the latest deadly outbreak of a haemorrhagic infection in Europe in 2011 was used for the case study. It was shown that this strain appeared on an intersection of two independent fluxes of horizontal gene exchange, one of which is a conventional for Enterobacteria stream of vectors generated in marine gamma-Proteobacteria; and the second is a new channel of antibiotic resistance genomic islands originated from environmental beta-Proteobacteria.

References

  1. Abe, T., Kanaya, S., Kinouchi, M., Ichiba, Y., Kozuki, T., et al., 2003. Informatics for unveiling hidden genome signatures. Genome Res. 13: 693-702.
  2. Brzuszkiewicz, E., Thürmer, A., Schuldes, J., Leimbach, A., Liesegang, H., et al., 2011. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch. Microbiol., doi:10.1007/s00203-011-0725-6.
  3. Ganesan, H., Rakitianskaia, A. S., Davenport, C. F., Tümmler, B., Reva, O. N. 2008. The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 9: 333.
  4. Langille, M. G., Brinkman, F. S., 2009. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25: 664-665.
  5. Lawrence, J. G., Ochman, H., 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44: 383-397.
  6. Levings, R. S., Partridge, S. R., Djordjevic, S. P., Hall, R. M., 2007. SGI1-K, a variant of the SGI1 genomic island carrying a mercury resistance region, in Salmonella enterica serovar Kentucky. Antimicrob. Agents Chemother. 51: 317-323.
  7. Manrique, M., Pareja-Tobes, P., Pareja-Tobes, E., Pareja, E., Tobes, R. 2011. Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system. Nut. Preceedings, doi:10.1038/npre.2011. 6001.1.
  8. Ramaiah, N., De, J., 2003. Unusual rise in mercuryresistant bacteria in coastal environs. Microb. Ecol. 45: 444-454.
  9. Reva, O. N., Tümmler, B., 2005. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics 6: 251.
  10. Van Passel, M. W., Bart, A., Luyf, A. C., van Kampen, A. H. van der Ende, A., 2006. The reach of the genome signature in prokaryotes. BMC Evol. Biol. 6: 84.
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Paper Citation


in Harvard Style

Bezuidt O., Mncube K. and N. Reva O. (2012). APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 118-123. DOI: 10.5220/0003704201180123


in Bibtex Style

@conference{bioinformatics12,
author={Oliver Bezuidt and Kingdom Mncube and Oleg N. Reva},
title={APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={118-123},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003704201180123},
isbn={978-989-8425-90-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange
SN - 978-989-8425-90-4
AU - Bezuidt O.
AU - Mncube K.
AU - N. Reva O.
PY - 2012
SP - 118
EP - 123
DO - 10.5220/0003704201180123