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Bioinformatics Advance Access originally published online on January 27, 2006
Bioinformatics 2006 22(8):905-910; doi:10.1093/bioinformatics/btl015
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen

A. M. Quirke , F. Jerry Reen , Marcus J. Claesson and E. Fidelma Boyd *

Department of Microbiology, University College Cork, National University of Ireland Cork, Ireland

*To whom correspondence should be addressed.

Genomic islands (GIs) are large chromosomal regions present in a subset of bacterial strains that increase the fitness of the organism under specific conditions. We compared the complete genome sequences of two Vibrio vulnificus strains YJ016 and CMCP6 and identified 14 regions (ranging in size from 14 to 117 kb), which had the characteristics of GIs. Bioinformatic analysis of these 14 GI regions identified the presence of phage-like integrase genes, aberrant GC content and genome signature (dinucleotide frequency) within each GI compared with the core genome indicating that these regions were acquired from an anomalous source. We examined the distribution of the nine GIs from strain YJ016 among 27 V.vulnificus isolates and found that most GIs were absent from the majority of these isolates. The chromosomal insertion sites of three GIs were adjacent to tRNA sites, which contained novel horizontally acquired DNA in all six available sequenced Vibrionaceae genomes.

Contact: f.boyd{at}ucc.ie

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on October 14, 2005; revised on December 19, 2005; accepted on January 20, 2006

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