Codon usage trend in mitochondrial CYB gene

• Nucleotide composition suggests MT-CYB gene is AT rich and C/A ending codons are more preferred in pisces, aves and mammals.
• Mean value of ENC was high which indicates low codon usage bias but CAI value was high suggesting high expression of CYB gene vertebrates.
• Nonsignificant correlation between ENC and CAI suggests that nucleotide composition has very weak relationship with codon selection.
• Correlation coefficient between codon usage and GC3 was positive suggesting that GC ending codons positively influenced the GC3 content.
• Correspondence analysis (COA) suggests that both mutation pressure and natural selection affect the codon usage in CYB gene.

Here we reported the pattern of codon usage and the factors which influenced the codon usage pattern in mitochondrial cytochrome B (MT-CYB) gene among pisces, aves and mammals. The F1 axis of correspondence analysis showed highly significant positive correlation with nucleobases A3, C and C3 and significant negative correlation with T and T3 while F2 of correspondence analysis showed significant positive correlation with C and C3 and significant negative correlation with A and A3. From the neutrality plot, it was evident that the GC12 was influenced by mutation pressure and natural selection with a ratio of 0.10/0.90 = 0.11 in pisces, 0.024/0.976 = 0.0245 in aves and in mammals 0.215/0.785 = 0.273, which indicated that the role of natural selection was more than mutation pressure on structuring the bases at the first and second codon positions. Natural selection played the major role; but compositional constraint and mutation pressure also played a significant role in codon usage pattern. Analysis of codon usage pattern has contributed to the better understanding of the mechanism of distribution of codons and the evolution of MT-CYB gene.

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