| Although synonymous codon usage in mammals has been investigated for decades, there are still controversial interpretations of the observed results. Selectionism cannot explain the strong regularities in the codon bias, while neutralism is unable to comprehend the unusual high frequency of G or C nucleotides (∼60%) in the third codon positions across all mammals. We performed a genome-wide computational analysis of synonymous codon usage with respect to local genomic GC-content, GC-content in the first and second codon positions, and overall genome length and GC-content. In this study, Codon Bias Index (CBI) is used to measure the codon bias in individual genes. The presented data is gathered from multiple available databases such as the Codon Usage Database, Animal Genome Size Database, BioGPS, and Exon/Intron Database. Our results suggest that local GC-content is a major contributor to the non-randomness of codon usage in mammals. Based on the obtained results, we propose a united hypothesis for the origin of GC-rich, GC-poor isochors and codon bias in mammals and vertebrates. |
