title: Vertebrate codon bias indicates a highly GC-rich ancestral genome.
abstract: Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences.
authors: Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Maryam.Nabiyouni@rockets.utoledo.edu
authors: Maryam
authors: M
authors: Nabiyouni
authors: Ashwin
authors: A
authors: Prakash
authors: Alexei
authors: A
authors: Fedorov
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics*; D002645:Chickens; D003062:Codon / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D019143:Evolution, Molecular; D015870:Gene Expression; D016678:Genome; D006801:Humans; D009154:Mutation; D009711:Nucleotides / Q000737:chemistry / Q000235:genetics; D016366:Open Reading Frames; D012641:Selection, Genetic; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish
chemical_list: D003062:Codon; D009711:Nucleotides