Codon bias patterns in photosynthetic genes of halophytic grass Aeluropus littoralis

Abstract

Codon bias refers to the differences in the frequency of occurrence of synonymous codons in coding DNA. Pattern of codon and optimum codon utilization is significantly different between the lives. This difference is due to the long term function of natural selection and evolution process. Genetics drift, mutation and regulation of gene expression are the main reasons for codon bias. In this study, the codon bias analysis was done on photosynthesis and respiratory related genes of phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), pyruvate orthophosphate dikinase (PPDK), glycerate kinase (GK) (nuclear genes), rubisco, NADH-dehydrogenase subunit F and cytochrome-C (chloroplast genes) from Aeluropus littoralis plant. Nuclear gene sequences were obtained after partial isolation and for chloroplast genes obtained from nucleotide database. Calculation of codon adaptation index (CAI) showed that studied genes with direct or indirect association with photosynthesis, had high level of gene expression and had also a tendency to optimum codon utilization. The results also showed the difference in codon bias between genes encoded in nucleus and chloroplast for some amino acids.

Keywords

• Codon bias
• Photosynthesis genes
• Codon adaptation index
• Aeluropus littoralis