Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
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.
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.
The CGS method may be an improvement over existing surrogate methods to detect genes of foreign origin.
- blah 12864_2011_4356_MOESM1_ESM.pdf (127KB)
- blah 12864_2011_4356_MOESM2_ESM.xls (73KB)
- blah 12864_2011_4356_MOESM3_ESM.xls (11551KB)
- blah 12864_2011_4356_MOESM4_ESM.pdf (68KB)
- blah 12864_2011_4356_MOESM5_ESM.pdf (61KB)
- blah 12864_2011_4356_MOESM6_ESM.pdf (61KB)
- blah 12864_2011_4356_MOESM7_ESM.pdf (61KB)
- blah 12864_2011_4356_MOESM8_ESM.pdf (78KB)
- blah 12864_2011_4356_MOESM9_ESM.pdf (60KB)
- blah 12864_2011_4356_MOESM10_ESM.pdf (562KB)
- blah 12864_2011_4356_MOESM11_ESM.pdf (159KB)
- blah 12864_2011_4356_MOESM12_ESM.pdf (8KB)
- Detection of horizontal transfer of individual genes by anomalous oligomer frequencies
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
- Online Date
- June 2012
- Online ISSN
- BioMed Central
- Additional Links
- Industry Sectors
- Author Affiliations
- 1. Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
- 2. Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- 3. Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA, 92093, USA