Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that low- and high-GC content genes with different codon usage occur frequently in the genome. The results of neutrality, correspondence, and correlation analyses indicated that mutational pressure and selective constraint were the main factors in shaping codon usage. Coding sequence length and the hydrophobicity of each protein were also identified as influences on codon usage bias, although their effect was minor. In addition, 27 codons, defined as optimal codons, might provide useful information for gene engineering, gene prediction, and molecular evolution studies.