Synonymous codon usage pattern in mitochondrial CYB gene in pisces, aves, and mammals

Area of Science:

• Mitochondrial genomics
• Molecular evolution
• Bioinformatics

Background:

• Cytochrome b (CYB) is crucial for mitochondrial complex III in oxidative phosphorylation.
• Codon usage bias describes the non-uniform selection of synonymous codons.
• Understanding codon usage patterns provides insights into evolutionary pressures.

Purpose of the Study:

• To investigate the codon usage patterns in the MT-CYB gene across different vertebrate classes (Pisces, Aves, Mammalia).
• To identify nucleotide composition biases and preferred codons at the third position.
• To determine the primary evolutionary forces driving codon usage variation.

Main Methods:

• Analysis of nucleotide composition (%C, %T, %A, %G) in MT-CYB genes.
• Evaluation of Relative Synonymous Codon Usage (RSCU) values and heat map visualization.
• Identification of absent codons in specific taxa.
• Correlation analysis to assess the impact of mutation pressure and natural selection.

Main Results:

• Distinct nucleotide composition biases were observed in Pisces (C/T-rich), Aves (A/C-rich), and Mammals (A/T-rich).
• RSCU analysis indicated a preference for A/C at the third codon position and avoidance of T/G.
• Low codon usage bias was detected across all three vertebrate classes.
• Leucine was the most frequent amino acid, while cysteine was the least frequent.

Conclusions:

• Mutation pressure is the predominant factor shaping MT-CYB codon usage patterns in fish, birds, and mammals.
• While natural selection may play a role, its influence is less significant compared to mutation pressure.
• The findings contribute to understanding the evolutionary dynamics of mitochondrial genes.