Guanine and Cytosine at the Second Codon Position Influence Gene Expression in Cereals

Abstract

The compositional variation and the codon usage bias of the coding sequences of genes were analyzed in five species of grass family i.e. Oryza sativa, Triticum aestivum, Sorghum bicolor, Hordeum vulgare and Zea mays along with two outlier species belonging to family Solanaceae viz. Lycopersicon esculentum and Nicotiana tabacum. Pyrimidine-skew and keto-skew values varied across the cereals. These two parameters showed moderate positive correlation with codon adaptation index which was used as a measure of gene expression and with the tRNA adaptation index commonly used as a measure of translational efficiency. These were further elucidated by regression analysis and adaptive codon enrichment analysis. The present analysis revealed that the guanine and cytosine content at second codon position influence the gene expression in cereal crops. Although the codon usage pattern in five cereals was similar but differed significantly from the outliers L. esculentum and N. tabacum.