Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among potamidids

Abstract

Codon usage bias (CUB) refers to an unequal occurrence of specific synonymous codons in a genome with variations within and among species. Findings suggest that CUB is significant in interpreting evolutionary trends of species and/or genes. However, information of CUB remained unclear for organisms in the family Potamididae. This study examined compositional features and codon usage patterns of coI gene among potamidids to identify factors shaping CUB. Quantification of CUB and the identification of causative factors were performed by assessing nucleotide composition, effective number of codons (ENC), relative synonymous codon usage (RSCU), parity rule (PR2) analysis and neutrality plot analysis as well as correspondence analysis (CoA). Results from neutrality plot suggested that natural selection is the dominant evolutionary factor for CUB in the coI gene among the different genera of potamidids. In contrast, CoA, PR2 and ENC analyses indicated the existence of mutational pressure with minor contribution. Nucleotide composition investigations indicated that most codons are AT rich; with T nucleotides count being highly presented. Thus, compositional restraint was also among the reasons behind the pattern of codon usage in coI gene of species in the potamidids. Although, the present study involved one mitochondrial gene, coI, the findings have demonstrated that various genera of potamidids are differentially adapted in the environment, and that coI gene may be differentially expressed and remain to be elucidated.