title: Codon usage trend in mitochondrial CYB gene.
abstract: 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.
authors.affiliation: Departments of Biotechnology, Assam University, Silchar 788011, Assam, India. Electronic address: arif.uddin29@gmail.com.
authors.forename: Arif
authors.initials: A
authors.lastname: Uddin
authors.affiliation: Departments of Biotechnology, Assam University, Silchar 788011, Assam, India. Electronic address: supriyoch_2008@rediffmail.com.
authors.forename: Supriyo
authors.initials: S
authors.lastname: Chakraborty
mesh_terms: D000818:Animals; D001482:Base Composition; D003062:Codon; D045303:Cytochromes b / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D024101:Mitochondrial Proteins / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D012641:Selection, Genetic; D014714:Vertebrates / Q000145:classification / Q000235:genetics*
chemical_list: D003062:Codon; D024101:Mitochondrial Proteins; D045303:Cytochromes b
keywords: Aves; Codon usage; MT-CYB gene; Mammals; Mutation pressure; Natural selection; Pisces