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

2012

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.

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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