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Open Access Highly Accessed Research article

A quantitative account of genomic island acquisitions in prokaryotes

Tom E Roos12 and Mark WJ van Passel3*

Author Affiliations

1 Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands

2 Netherlands Bioinformatics Centre, Nijmegen, The Netherlands

3 Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands

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BMC Genomics 2011, 12:427  doi:10.1186/1471-2164-12-427

Published: 24 August 2011

Abstract

Background

Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness.

In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species.

Results

When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor.

Conclusions

This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.

Keywords:
Genomic Islands; genome signature; horizontal gene transfer