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Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

Abstract

G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from 0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.

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Correspondence to Rintaro Saito.

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Open Access This is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License ( https://creativecommons.org/licenses/by-nc/2.0 ), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

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Suzuki, H., Saito, R. & Tomita, M. Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria. J Bioinform Sys Biology 2007, 61374 (2007). https://doi.org/10.1155/2007/61374

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  • DOI: https://doi.org/10.1155/2007/61374

Keywords

  • Codon
  • System Biology
  • Codon Usage
  • Synonymous Codon
  • Synonymous Codon Usage