Comparative analysis of codon usage of mitochondrial genomes provides evolutionary insights into reptiles

Abstract

Current available information on reptile genomes provides great potential for the study of unique adaptations from a genomic perspective. We compared differences in base composition and codon usage patterns across 400 reptile mitochondrial genomes assessing AT and GC skew, GC frequency, codon usage, effective number of codons, and codon adaptation index. We identified poor GC content in reptile mitochondrial genomes, with a predominant bias toward Adenine. We determined a compositional asymmetry between different taxonomic groups, which are inversely correlated to the rates of rearrangements in the mitogenome. We found that the most common codons in reptile mitochondrion are CTA (L), ATA (M) and ACA (T), which relates with have been found in birds, meaning that these patterns are shared across sauropsid mitogenomes. Codon usage bias clustering and effective codon number analyses revelated compositional asymmetry based on RSCU as well as that reptile mitogenomes are translationally efficient and are under selection pressure. Codon adaptation index revealed highest values in turtles indicating higher translational efficiency of mitochondrial genes among all reptiles, which could be related to metabolic adaptations (i.e., tolerance to anoxic conditions). This was also seen in other groups such as crocodiles (i.e., acclimation to cold) and snakes (phylogenetic origin of toxin-secreting oral glands and the evolutionary redesign of cytochrome c oxidase complex genes). We discuss our findings in the context of potential adaptations and evolutionary implications that these genomic differences provide to reptiles.