Comparative analysis of the mitochondrial genomes of two fish species Channa striata and Channa punctata using codon usage bias and their evolutionary relationship

Abstract Codon usage bias (CUB) occurs when certain codons are utilized more repeatedly than the other synonymous codons for the same amino acid in the coding sequences of genes. The investigation of CUB aids in the understanding of optimal codons, gene expression, protein production and trends of evolution. In our study, CUB was explored for the mitochondrial protein coding genes of Channa striata and Channa punctata, estimating their base contents, identifying over-represented and under-represented codons, and determining the factors contributing to the codon usage bias. The base compositions of the two fishes showed the trend C>T>A>G and the GC composition was in the order GC1>GC3>GC2. The average ENC value in both sets of coding sequences was >35, indicating a lower CUB. The mitochondrial genomes of the two fishes are AT-rich. In Channa striata, 8 codons were found to be over-represented, and 14 codons were under-represented. On the other hand, Channa punctata showed 9 over-represented codons and 18 under-represented codons across the coding sequences in mt-genome. Among the over-represented codons, CTA, ACC, AAA and GAA were found in Channa striataand not in Channa punctata. Whereas, the over-represented codons CTC, CAA, GTC, GAC and GGC were found in Channa punctata and not in Channa striata. The results suggested that both the evolutionary processes viz. selective pressure and mutation governed the codon usage arrangement in the mitochondrial genes of the two freshwater fishes.