Towards an accurate identification of mosaic genes and partial horizontal gene transfers
Abstract
Abstract Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a full-genome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution. © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. « Previous | Next Article » Table of Contents This Article Nucl. Acids Res. (2011) 39 (21): e144. doi: 10.1093/nar/gkr735 First published online: September 14, 2011 This article is Open Access OA » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Screen PDF Supplementary Data All Versions of this Article: gkr735v1 39/21/e144 most recent Classifications Methods Online Services Alert me when cited Alert me if corrected Alert me if commented Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Responses Submit a response No responses published Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Google Scholar Articles by Boc, A. Articles by Makarenkov, V. PubMed PubMed citation Articles by Boc, A. Articles by Makarenkov, V. 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