Detecting horizontally transferred and essential genes based on dinucleotide relative abundance

Robert H. Baran, Hanseok Ko

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)267-276
Number of pages10
JournalDNA Research
Volume15
Issue number5
DOIs
Publication statusPublished - 2008 Dec 1

Fingerprint

Essential Genes
Genome
Bacterial Genomes
Escherichia coli K12
Horizontal Gene Transfer
Conserved Sequence
Base Composition
Nucleotides
Bacteria
Genes

Keywords

  • Amelioration
  • Dinucleotide frequency
  • Essential genes
  • Horizontal transfer
  • Molecular evolution

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Detecting horizontally transferred and essential genes based on dinucleotide relative abundance. / Baran, Robert H.; Ko, Hanseok.

In: DNA Research, Vol. 15, No. 5, 01.12.2008, p. 267-276.

Research output: Contribution to journalArticle

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