Genome-wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

The biological phenomenon where some synonymous codons are repeatedly preferred to others in gene transcripts is called codon usage bias (CUB). The analysis of CUB is not only helpful in evolutionary biology but also in improving the expression level of exogenous genes in the host cell by codon optimization. The overall nucleotide composition analysis demonstrated an unequal distribution of four nucleobases and T% was the highest in all seven species. The genes were AT-rich, evident from overall low GC content. In addition, third codon position analysis indicated that in four Bombina species namely, Bombina fortinuptialis, Bombina lichuanensis, Bombina maxima, Bombina microdeladigitora, nucleobase A3/T3 was the preferred one, whereas A3/C3 was favored in Bombina bombina, Bombina orientalis, and Bombina variegata. Influence of mutation pressure on codon distribution and codon bias was evident from correlation analysis. Correspondence analysis demonstrated that compositional bias driven by mutation pressure along with natural selection acted on CUB of mitochondrial genes. Neutrality plot revealed that natural selection played a major role whereas mutation pressure had a minor but significant role. Our phylogenetic analyses showed that closely linked species belonging to the same genus were noticeably separated in different clades.