Lateral transfer of genes and gene fragments in prokaryotes

Chan, Cheong Xin, Beiko, Robert G., Darling, Aaron E. and Ragan, Mark A. (2009) Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution, 1 429-438. doi:10.1093/gbe/evp044


Author Chan, Cheong Xin
Beiko, Robert G.
Darling, Aaron E.
Ragan, Mark A.
Title Lateral transfer of genes and gene fragments in prokaryotes
Journal name Genome Biology and Evolution   Check publisher's open access policy
ISSN 1759-6653
Publication date 2009-11-01
Year available 2009
Sub-type Article (original research)
DOI 10.1093/gbe/evp044
Open Access Status DOI
Volume 1
Start page 429
End page 438
Total pages 10
Editor Martin, W.
Place of publication Oxford, U. K.
Publisher Oxford University Press
Language eng
Subject C1
970106 Expanding Knowledge in the Biological Sciences
060408 Genomics
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 analyze 1,462 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 1,462 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 nonpathogens. As ORB+ gene sets are about 50% more common than 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.
Keyword Lateral genetic transfer
Horizontal genetic transfer
Genetic recombination
Genome evolution
Comparative genomics
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID CE0348221
DBI-0630765
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
 
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Created: Fri, 05 Feb 2010, 01:37:28 EST by Susan Allen on behalf of Institute for Molecular Bioscience