Codon usage bias and purifying selection identified in Cirrhinus reba mitogenome

Abstract

In our previous study, we described sequence assembly and organization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba (GenBank accession no.: MN862482). In this study, our attempts were to find out any mutation or selection pressures and codon usage patterns existing in the mitogenome of the same fish. We applied bioinformatics tools to measure important gene parameters including AT/GC skewness, codon adaptation index (CAI), the effective number of codons (ENc) and GC percentages of each protein coding gene. We found an overrepresentation of A and C resulting a lower number of T and G bases, respectively, where AT-skew was slightly positive and GC-skew was slightly negative. Except for ND6, all protein coding genes (PCGs) had negative GC-skew, which indicated the higher occurrence of Cs. With reference to other two mitogenomes, the dN/dS or Ka/Ks ratios ranged from the lowest value (0.016) for ND4L to the highest value (0.694) for ND1 gene which indicated that PCGs of this fish evolved under strong purifying selection. We further analyzed the codon frequency and relative synonymous codon usage (RSCU) and observed a total of 3802 codons which were used for coding 20 amino acids by a standard set of 64 codons. The amino acids Leucine and Serine were encoded each by six different codons, whereas rest of the amino acids was encoded by either two or four codons. We identified a total of 25 RSCU values (> 1) and revealed 12 codons as “overpresented” that implied for codon usage bias to engage in highly expressed genes for efficient protein synthesis via translational selection. The existence of codon usage biasness rolling in translational selection and the signs of purifying selection identified in PCGs suggest obvious conservation of this threatened fish species.