Limitations of compositional approach to identifying horizontally transferred genes |
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Authors: | Wang B |
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Institution: | (1) Institute of Theoretical Physics, Chinese Academy of Sciences, P.O. Box 2735, Beijing 100080, PR China State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, P.O. Box 2719, Beijing 100080, PR China, CN |
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Abstract: | Genes with atypical G+C content and pattern of codon usage in a certain genome are possibly of exotic origin, and this idea
has been applied to identify horizontal events. In this way, it was postulated that a total of 755 genes in the E. coli genome are relics of horizontal events after the divergence of E. coli from the Salmonella lineage 100 million years ago (Lawrence and Ochman, 1998). In this paper we propose a new way to study sequence composition
more thoroughly. We found that although the 755 genes differ in composition from other genes in the E. coli genome, the difference is minor. If we accepted that these genes are horizontally transferred, then (1) it would be more
likely that they were transferred from genomes evolutionarily closely related to E. coli; but (2) the dating method used by Lawrence and Ochman (1997, 1998) largely underestimated the average age of introduced sequences
in the E. coli genome, in particular, most of the 755 genes should be introduced into E. coli before, instead of after, the divergence of E. coli from the Salmonella lineage. Our study reveals that atypical G+C content and pattern of codon usage are not reliable indicators of horizontal
gene transfer events.
Received: 27 September 2000 / Accepted: 9 April 2001 |
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Keywords: | : Horizontal transfer — Compositional characteristics — G+C content — Pattern of codon usage — Escherichia coli— Sequence amelioration — Substitution |
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