Detection of horizontal transfer of individual genes by anomalous oligomer frequencies

<p>Abstract</p> <p>Background</p> <p>Understanding the history of life requires that we understand the transfer of genetic material across phylogenetic boundaries. Detecting genes that were acquired by means other than vertical descent is a basic step in that process. D...

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Main Authors: Elhai Jeff, Liu Hailan, Taton Arnaud
Format: Article
Language:English
Published: BMC 2012-06-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/13/245
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spelling doaj-0cd35ed0d6e34901b9e26995efa0e44d2020-11-24T21:24:42ZengBMCBMC Genomics1471-21642012-06-0113124510.1186/1471-2164-13-245Detection of horizontal transfer of individual genes by anomalous oligomer frequenciesElhai JeffLiu HailanTaton Arnaud<p>Abstract</p> <p>Background</p> <p>Understanding the history of life requires that we understand the transfer of genetic material across phylogenetic boundaries. Detecting genes that were acquired by means other than vertical descent is a basic step in that process. Detection by discordant phylogenies is computationally expensive and not always definitive. Many have used easily computed compositional features as an alternative procedure. However, different compositional methods produce different predictions, and the effectiveness of any method is not well established.</p> <p>Results</p> <p>The ability of octamer frequency comparisons to detect genes artificially seeded in cyanobacterial genomes was markedly increased by using as a training set those genes that are highly conserved over all bacteria. Using a subset of octamer frequencies in such tests also increased effectiveness, but this depended on the specific target genome and the source of the contaminating genes. The presence of high frequency octamers and the GC content of the contaminating genes were important considerations. A method comprising best practices from these tests was devised, the Core Gene Similarity (CGS) method, and it performed better than simple octamer frequency analysis, codon bias, or GC contrasts in detecting seeded genes or naturally occurring transposons. From a comparison of predictions with phylogenetic trees, it appears that the effectiveness of the method is confined to horizontal transfer events that have occurred recently in evolutionary time.</p> <p>Conclusions</p> <p>The CGS method may be an improvement over existing surrogate methods to detect genes of foreign origin.</p> http://www.biomedcentral.com/1471-2164/13/245
collection DOAJ
language English
format Article
sources DOAJ
author Elhai Jeff
Liu Hailan
Taton Arnaud
spellingShingle Elhai Jeff
Liu Hailan
Taton Arnaud
Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
BMC Genomics
author_facet Elhai Jeff
Liu Hailan
Taton Arnaud
author_sort Elhai Jeff
title Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
title_short Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
title_full Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
title_fullStr Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
title_full_unstemmed Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
title_sort detection of horizontal transfer of individual genes by anomalous oligomer frequencies
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2012-06-01
description <p>Abstract</p> <p>Background</p> <p>Understanding the history of life requires that we understand the transfer of genetic material across phylogenetic boundaries. Detecting genes that were acquired by means other than vertical descent is a basic step in that process. Detection by discordant phylogenies is computationally expensive and not always definitive. Many have used easily computed compositional features as an alternative procedure. However, different compositional methods produce different predictions, and the effectiveness of any method is not well established.</p> <p>Results</p> <p>The ability of octamer frequency comparisons to detect genes artificially seeded in cyanobacterial genomes was markedly increased by using as a training set those genes that are highly conserved over all bacteria. Using a subset of octamer frequencies in such tests also increased effectiveness, but this depended on the specific target genome and the source of the contaminating genes. The presence of high frequency octamers and the GC content of the contaminating genes were important considerations. A method comprising best practices from these tests was devised, the Core Gene Similarity (CGS) method, and it performed better than simple octamer frequency analysis, codon bias, or GC contrasts in detecting seeded genes or naturally occurring transposons. From a comparison of predictions with phylogenetic trees, it appears that the effectiveness of the method is confined to horizontal transfer events that have occurred recently in evolutionary time.</p> <p>Conclusions</p> <p>The CGS method may be an improvement over existing surrogate methods to detect genes of foreign origin.</p>
url http://www.biomedcentral.com/1471-2164/13/245
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