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Title: A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.
Authors: Ou, Hong-Yu
Chen, Ling-Ling
Lonnen, James
Chaudhuri, Roy R.
Thani, Ali Bin
Smith, Rebecca J.
Garton, Natalie J.
Hinton, Jay
Pallen, Mark
Barer, Michael R.
Rajakumar, Kumar
First Published: 2006
Publisher: Oxford University Press (OUP)
Citation: Nucleic Acids Research, 2006, 34(1), e3
Abstract: We devised software tools to systematically investigate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach identified 49 GIs occupying ∼1.7 Mb that mapped to 18 tRNA genes, missing 2 but identifying a further 30 GIs as compared with Islander [Y. Mantri and K. P. Williams (2004), Nucleic Acids Res., 32, D55–D58]. All these GIs had many strain-specific CDS, anomalous GC contents and/or significant dinucleotide biases, consistent with foreign origins. Our analysis demonstrated marked conservation of sequences flanking both empty tRNA sites and tRNA-associated GIs across all four genomes. Remarkably, there were only 2 upstream and 5 downstream deletions adjacent to the 328 loci investigated. In silico PCR analysis based on conserved flanking regions was also used to interrogate hotspots in another eight completely or partially sequenced E.coli and Shigella genomes. The tools developed are ideal for the analysis of other bacterial species and will lead to in silico and experimental discovery of new genomic islands.
DOI Link: 10.1093/nar/gnj005
ISSN: 0305-1048
eISSN: 1362-4962
Version: Publisher version
Status: Peer reviewed
Type: Article
Rights: Copyright © The Authors 2006. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact
Appears in Collections:Published Articles, Dept. of Infection, Immunity and Inflammation

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