Analysis of Codon Usage Bias and Nucleotide Composition of Mitochondrial Genomes of the Tuatara (Sphenodon punctatus)

The concept of codon usage bias (CUB) occurs when certain codons are utilized more repeatedly than the other synonymous codons for an amino acid. The investigation of CUB aids in the understanding of optimal codons, gene expression, protein production and trends of evolution. Tuatara has two mitochondrial genomes designated as tuatara mitochondrial genome 1 (TMG1) and tuatara mitochondrial genome 2 (TMG2). In our study, an in-house software was used to explore the CUB of TMG1 and TMG2, estimating their base contents, identifying overrepresented and underrepresented codons, and determining the factors contributing to the codon usage bias. The TMG1 and TMG2's base compositions showed the trend A>T>C>G and the GC composition was in the order GC1>GC2>GC3. The average ENC value in both sets of coding sequences was >35, indicating a lower CUB. Tuatara mitochondrial genomes are AT-rich. In TMG1, nine codons were found to be overrepresented, and nineteen codons were found to be underrepresented. On the other hand, TMG2 showed seventeen overrepresented codons and twenty-three underrepresented codons across the coding sequences of mt-genome. The results suggested that both the evolutionary processes namely, selective pressure and mutation governed the codon usage arrangement in the genes of tuatara mt-genomes.