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Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

Kanhere, A; Vingron, M; (2009) Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC EVOL BIOL , 9 , Article 9. 10.1186/1471-2148-9-9. Green open access

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Abstract

Background: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.Results: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.Conclusion: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.

Type: Article
Title: Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2148-9-9
Publisher version: http://dx.doi.org/10.1186/1471-2148-9-9
Language: English
Additional information: © 2009 Kanhere and Vingron; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: TRANSFER-RNA SYNTHETASES, GENOMIC SIGNATURE, TRANSFER EVENTS, EVOLUTION, TREE, LIFE, QUANTIFICATION, RECONSTRUCTION, REGRESSION, BACTERIA
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/1330683
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