Full Paper New insights into the interplay between codon bias determinants in plants

Codon bias is the non-randomuse of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mu-tational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage pro-files. Neutral forces such asmutational pressure andG|C-biased gene conversion appeared to under-lie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences be-tween monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias. Key words: codon bias, mutational bias, translational selection, plant genetics 1