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Genome Biology and Evolution Advance Access published online on November 4, 2009
Genome Biology and Evolution, doi:10.1093/gbe/evp044
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Lateral transfer of genes and gene fragments in prokaryotes

Cheong Xin Chan1,3, Robert G. Beiko1,2, Aaron E. Darling1,4 and Mark A. Ragan1,*

1 The University of Queensland, Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, Brisbane, Queensland 4072, Australia
2 Dalhousie University, Department of Computer Science, 6050 University Avenue, Halifax, Nova Scotia, Canada B3H 1W5

* Author for Correspondence: Mark Ragan, The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia, tel +61-7-3346-2616, fax +61-7-3346-2101, m.ragan{at}uq.edu.au


  Abstract

Lateral genetic transfer (LGT) involves the movement of genetic material from one lineage into another, and its subsequent incorporation into the new host genome via genetic recombination. Studies in individual taxa have indicated lateral origins for stretches of DNA of greatly varying length, from a few nucleotides to chromosome size. Here we analyse 1462 sets of single-copy, putatively orthologous genes from 144 fully sequenced prokaryote genomes, asking to what extent complete genes and fragments of genes have been transferred and recombined in LGT. Using a rigorous phylogenetic approach, we find evidence for LGT in at least 476 (32.6%) of these 1462 gene sets: 286 (19.6%) clearly show one or more observable recombination breakpoints within the boundaries of the open reading frame, while a further 190 (13.0%) yield trees that are topologically incongruent with the reference tree but do not contain a recombination breakpoint within the open reading frame. We refer to these gene sets as observable recombination breakpoint positive (ORB+) and negative (ORB-) respectively. The latter are prima facie instances of lateral transfer of an entire gene or beyond. We observe little functional bias between ORB+ and ORB- gene sets, but find that incorporation of entire genes is potentially more frequent in pathogens than in non-pathogens. As ORB+ gene sets are almost twice as common as ORB- sets in our data, the transfer of gene fragments has been relatively frequent, and the frequency of LGT may have been systematically underestimated in phylogenetic studies.

Keywords: lateral genetic transfer, horizontal genetic transfer, genetic recombination, genome evolution, comparative genomics

Received August 25, 2009; Revised October 13, 2009; Accepted October 31, 2009

3 Present address: Rutgers University, Department of Ecology, Evolution, and Natural Resources, New Brunswick, NJ 08901, USA

4 Present address: University of California Davis, Genome Center, Davis, CA 95616, USA


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