Compositional features and pattern of codon usage for mitochondrial CO genes among reptiles

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Codon usage bias (CUB) describes the non-random occurrence of synonymous nucleotide triplets in gene coding sequences.
• Mitochondrial genes (COI, COII, COIII) are crucial for cellular respiration and evolutionary studies.

Purpose of the Study:

• To analyze the compositional patterns and codon usage bias of COI, COII, and COIII genes across different reptile orders.
• To investigate the evolutionary forces driving codon usage in these reptilian mitochondrial genes.

Main Methods:

• Bioinformatic analysis of nucleotide composition and codon usage patterns.
• Estimation of base composition, GC content at codon positions, SCUO, and RSCU values.
• Application of neutrality plots, mutational responsive index, translational selection, correspondence analysis, parity plots, and correlation studies.

Main Results:

• Reptilian CO genes exhibit uneven nucleotide usage, with a high A content and low G content, showing a prominent AT bias.
• GC1 percentage was highest across all three CO genes in the studied reptiles.
• Relative synonymous codon usage (RSCU) indicated a preference for A-ending codons.
• Lower Scaled Constraint on Usage (SCUO) values suggested weaker CUB with variations across genes and orders.

Conclusions:

• Natural selection is identified as the primary evolutionary force shaping CUB in reptilian COI, COII, and COIII genes.
• Mutation pressure also contributes to the evolutionary dynamics of these mitochondrial genes in reptiles.
• The findings provide insights into the molecular evolution of mitochondrial genomes in reptiles.