Journal Article

Detecting Horizontally Transferred and Essential Genes Based on Dinucleotide Relative Abundance

Robert H. Baran and Hanseok Ko

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 15, issue 5, pages 267-276
Published in print October 2008 | ISSN: 1340-2838
Published online September 2008 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsn021

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Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.

Keywords: amelioration; dinucleotide frequency; essential genes; horizontal transfer; molecular evolution

Journal Article.  6132 words.  Illustrated.

Subjects: Genetics and Genomics

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