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MBE Advance Access published online on July 7, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl053
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted June 14, 2006

Research Article

A Computational Tool for the Genomic Identification of Regions of Unusual Compositional Properties and its Utilization in the Detection of Horizontally Transferred Sequences

Catherine Putonti 1, Yi Luo 2, Charles Katili 2, Sergey Chumakov 3, George E. Fox 4, Dan Graur 5 *, and Yuriy Fofanov 1

1 Department of Computer Science, University of Houston, Houston, Texas 77204-3010, USA; Department of Biology and Biochemistry, University of Houston, Houston TX 77204-5001, USA
2 Department of Computer Science, University of Houston, Houston, Texas 77204-3010, USA
3 Department of Computer Science, University of Houston, Houston, Texas 77204-3010, USA; Department of Physics, University of Guadalajara, Guadalajara, Jalisco 44420, Mexico
4 Department of Biology and Biochemistry, University of Houston, Houston TX 77204-5001, USA; Department of Chemical Engineering, University of Houston, Houston TX 77204-4004, USA
5 Department of Biology and Biochemistry, University of Houston, Houston TX 77204-5001, USA

* To whom correspondence should be addressed.
Dan Graur, E-mail: dgraur{at}uh.edu


  Abstract

Similarity Plot (S-plot) is a Windows-based application for large-scale comparisons and 2D visualization of compositional similarities between genomic sequences. This application combines two approaches widely used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in identifying highly similar regions between genomes as well as regions with unusual compositional properties (RUCPs) within a single genome, which may be indicative of horizontal gene transfer or of locus specific selective forces. We use S-plot to identify regions that may have originated through horizontal gene transfer through a two-step approach, by first comparing a genomic sequence to itself and, subsequently, comparing it to the genomic sequence of a closely related taxon. Moreover, by comparing these suspect sequences to one another, we can estimate a minimum number of sources for these putative xenologous sequences. We illustrate the uses of S-Plot in a comparison involving Escherichia coli K12 and E. coli O157:H7. In O157:H7, we found 145 regions that have most probably originated through horizontal gene transfer. By using S-plot to compare each of these regions to 277 completely sequenced prokaryotic genomes, one sequence was found to have similar compositional properties to the Yersinia pseudotuberculosis genome, indicating a transfer from a Yersinia or Yersinia relative. Based upon our analysis of RUCPs in O157:H7, we infer that there were at least 53 sources of horizontally transferred sequences.

Keywords: horizontal (lateral) gene transfer; sequence composition.
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