Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

• Published in: Korean journal of parasitology 2017, Hosts and Diseases, 55(2), , pp.175-183
• Main Author: Bae, Young-An
• Format: Article
• Language: English
• Subjects: Animals; Base Composition; Clonorchis sinensis - enzymology; Clonorchis sinensis - genetics; Codon - chemistry; Codon - genetics; Evolution, Molecular; Genome, Helminth - genetics; Monophenol Monooxygenase - genetics; Monophenol Monooxygenase - physiology; Original; Selection, Genetic; 예방의학
• ISSN: 0023-4001; 2982-5164; 1738-0006; 2982-6799
• DOI: 10.3347/kjp.2017.55.2.175

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC and GC was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the and genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed genes, than in poorly expressed genes.