title: Patterns of synonymous codon usage bias in the model  grass Brachypodium distachyon.
abstract: 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.
authors.affiliation: College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan, China.
authors.forename: H
authors.initials: H
authors.lastname: Liu
authors.forename: Y
authors.initials: Y
authors.lastname: Huang
authors.forename: X
authors.initials: X
authors.lastname: Du
authors.forename: Z
authors.initials: Z
authors.lastname: Chen
authors.forename: X
authors.initials: X
authors.lastname: Zeng
authors.forename: Y
authors.initials: Y
authors.lastname: Chen
authors.forename: H
authors.initials: H
authors.lastname: Zhang
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D058431:Brachypodium / Q000235:genetics*; D003062:Codon; D015870:Gene Expression; D057927:Hydrophobic and Hydrophilic Interactions; D015999:Multivariate Analysis; D016366:Open Reading Frames; D010940:Plant Proteins / Q000235:genetics*
chemical_list: D003062:Codon; D010940:Plant Proteins