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MBE Advance Access originally published online on July 7, 2006
Molecular Biology and Evolution 2006 23(10):1863-1868; 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

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*,{dagger}, Yi Luo*, Charles Katili*, Sergey Chumakov*,{ddagger}, George E. Fox{dagger},§, Dan Graur{dagger} and Yuriy Fofanov*,{dagger}

* Department of Computer Science, University of Houston; {dagger} Department of Biology and Biochemistry, University of Houston; {ddagger} Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico; and § Department of Chemical Engineering, University of Houston

E-mail: dgraur{at}uh.edu.

Similarity Plot (S-plot) is a Windows-based application for large-scale comparisons and 2-dimensional visualization of compositional similarities between genomic sequences. This application combines 2 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 2-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 with 277 completely sequenced prokaryotic genomes, 1 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.

Key Words: horizontal (lateral) gene transfer • sequence composition • Escherichia coli K12 • Escherichia coli O157:H7


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