Research article

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

Aditi Kanhere^1,2 and Martin Vingron¹

¹Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany

²MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London W1T 4JF, UK

author email corresponding author email

BMC Evolutionary Biology 2009, 9:9doi:10.1186/1471-2148-9-9

Published:	10 January 2009

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.