Analysis of synonymous codon usage in Zea mays

Abstract

It is important and meaningful to understand the codon usage pattern and the factors that shape codon usage of maize. In this study, trends in synonymous codon usage in maize have been firstly examined through the multivariate statistical analysis on 7402 cDNA sequences. The results showed that the genes positions on the primary axis were strongly negatively correlated with GC3s, GC content of individual gene and gene expression level assessed by the codon adaptation index (CAI) values, which indicated that nucleotide composition and gene expression level were the main factors in shaping the codon usage of maize, and the variation in codon usage among genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. At the same time, CDS length and the hydrophobicity of each protein were, respectively, significantly correlated with the genes locations on the primary axis, GC3s and CAI values. We infer that genes length and the hydrophobicity of the encoded protein may play minor role in shaping codon usage bias. Additional 28 codons ending with a G or C base have been defined as "optimal codons", which may provide useful information for maize gene-transformation and gene prediction.

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

“…All CDSs were extracted by writing a C program. A check of CDS applicability was performed based on the following criteria: 1) to minimize sampling error, each CDS was ≥100 codons long; 2) each CDS had the proper initial codon at the beginning and termination codon at the end and lacked an intermediate stop codon; 3) exact duplicated sequences were detected and excluded from the dataset Liu et al, 2010). The final dataset contained 24,439 CDSs.…”

“…The codon adaptation index (CAI) is used to predict the level of gene expression and assess the extent to which selection has been effective in molding the pattern of codon usage (Sharp and Li, 1987;Naya et al, 2001;Gupta et al, 2004). In this study, the CAI value for every gene was calculated, and the genes coding ribosomal proteins were used as reference sequence (Liu et al, 2004;Liu et al, 2010).…”

“…The 2 groups of datasets, which were regarded as the high-and low-bias gene datasets, were 5% of the total genes located at the extreme right and left of axis 1 produced by correspondence analysis on RSCU, respectively . Codons with a frequency of usage that was significantly higher (P < 0.01) in high-bias genes than that in genes with low bias were defined as the optimal codons (Liu et al, 2010). SPSS 12.0 was implemented for statistical analysis.…”

“…For the vast majority organisms, biased codon usage is primarily a result of mutational pressure or natural selection (Eyre-Walker, 1991;Stenico et al, 1994;Duret and Mouchiroud, 1999;Morton and Wright, 2007;Wang and Hickey, 2007;Jiang et al, 2008;Roychoudhury and Mukherjee, 2010). In plants, most studies on codon usage bias to date have focused on model plants and important food crops, such as Arabidopsis thaliana, Oryza sativa, Zea mays, and T. aestivum (Liu et al, 2004;Morton and Wright, 2007;Wang and Hickey, 2007;Zhang et al, 2007;Liu et al, 2010). For these organisms, the features of codon choice show some diversity, but the main factors influencing codon usage bias are base compositional mutation bias and selection to increase translation efficiency.…”

Mutational Pressure Drives Evolution of Synonymous Codon Usage in Genetically Distinct Oenothera plastomes

“…This suggested clearly that gene expression level also has considerable influence in SCU variation across PCGs. Influence of gene expression levels on SCUB in plant genes was recently reported in Zea mays (56) and also in Oncidium ramsey (34). Significant negative correlations of axis 2 with T 3, and axis 3 with GC 3 in all Oenothera species suggest the influence of T 3 and GC 3 contents in framing SCUB.…”