Species-dependent differences in codon usage are well known, 8 but recent studies have identified variations within species that must also be addressed by the neutralist and selective models. the choice among synonymous codons may reflect a balance between selective and mutational pressures. These models are not mutually exclusive, i.e. In contrast, the possibility of translational selection has led to the selective model, in which the choice of synonymous codons reflects tRNA abundance 5 to optimize the efficiency 4 and accuracy 6 of translation. The possibility that mutational bias affects codon usage has led to the neutralist model, in which codon identity is mainly determined by nucleotide substitution patterns in the genome. 1– 4 The non-random use of synonymous codons is known as codon bias, and it may reflect several underlying factors, including mutational bias in the genome and translational selection. The genetic code is redundant, with most amino acids encoded by two or more synonymous codons. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy.

The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals.

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