Abstract
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.
Original language | English (US) |
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Pages (from-to) | 1863-1868 |
Number of pages | 6 |
Journal | Molecular Biology and Evolution |
Volume | 23 |
Issue number | 10 |
DOIs | |
State | Published - Oct 2006 |
Keywords
- Escherichia coli K12
- Escherichia coli O157:H7
- Horizontal (lateral) gene transfer
- Sequence composition
ASJC Scopus subject areas
- Genetics
- Biochemistry
- Genetics(clinical)
- Biochemistry, Genetics and Molecular Biology(all)
- Ecology, Evolution, Behavior and Systematics
- Agricultural and Biological Sciences (miscellaneous)
- Molecular Biology