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Applied Bioinformatics

, Volume 3, Issue 4, pp 219–228 | Cite as

Genomic Conflict Settled in Favour of the Species Rather Than the Gene at Extreme GC Percentage Values

  • Shang-Jung Lee
  • James R. Mortimer
  • Donald R. ForsdykeEmail author
Original Research

Abstract

Wada and colleagues have shown that, whether prokaryotic or eukaryotic, each gene has a ‘homostabilising propensity’ to adopt a relatively uniform GC percentage (GC%). Accordingly, each gene can be viewed as a ‘microisochore’ occupying a discrete GC% niche of relatively uniform base composition amongst its fellow genes. Although first, second and third codon positions usually differ in GC%, each position tends to maintain a uniform, gene-specific GC% value. Thus, within a genome, genic GC% values can cover a wide range. This is most evident at third codon positions, which are least constrained by amino acid encoding needs. In 1991, Wada and colleagues further noted that, within a phylogenetic group, genomic GC% values can also cover a wide range. This is again most evident at third codon positions. Thus, the dispersion of GC% values among genes within a genome matches the dispersion of GC% values among genomes within a phylogenetic group. Wada described the context-independence of plots of different codon position GC% values against total GC% as a ‘universal’ characteristic. Several studies relate this to recombination. We have confirmed that third codon positions usually relate more to the genes that contain them than to the species. However, in genomes with extreme GC% values (low or high), third codon positions tend to maintain a constant GC%, thus relating more to the species than to the genes that contain them. Genes in an extreme-GC% genome collectively span a smaller GC% range, and mainly rely on first and second codon positions for differentiation as ‘microisochores’. Our results are consistent with the view that differences in GC% serve to recombinationally isolate both genome sectors (facilitating gene duplication) and genomes (facilitating genome duplication, e.g. speciation). In intermediate-GC% genomes, conflict between the needs of the species and the needs of individual genes within that species is minimal. However, in extreme-GC% genomes there is a conflict, which is settled in favour of the species (i.e. group selection) rather than in favour of the gene (genic selection).

Keywords

Codon Position Prokaryotic Genome Mutational Bias Codon Usage Table Thermal Denaturation Study 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

Queen’s University hosts the webpages of DRF where full-text versions of some of the cited references may be found ( http://post.queensu.ca/~forsdyke/homepage.htm ). No sources of funding were used to assist in the preparation of this study. The authors have no conflicts of interest that are directly relevant to the content of this article.

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Copyright information

© Adis Data Information BV 2004

Authors and Affiliations

  • Shang-Jung Lee
    • 1
  • James R. Mortimer
    • 2
  • Donald R. Forsdyke
    • 3
    Email author
  1. 1.Genetics Graduate ProgramUniversity of British ColumbiaVancouverCanada
  2. 2.Merck-Frosst CanadaMontrealCanada
  3. 3.Department of BiochemistryQueen’s UniversityKingstonCanada

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