title: Synonymous codon usage pattern in mitochondrial CYB gene in pisces, aves, and mammals.
abstract: Cytochrome b (CYB) protein plays an important role in complex III of the mitochondrial oxidative phosphorylation. Codon usage is the phenomenon of non-uniform usage of synonymous codons. In the present study, we report the pattern of codon usage in MT-CYB gene using various codon usage parameters. Nucleotide composition such as % of C and T was higher than A and G in pisces. In aves, % of A and C was higher than T and G but in mammals, A and T was higher than C and G. Heat map shows that AT-ending codons were mostly negative and GC-ending codons were mostly positive. From the heat map based on RSCU values, it is evident that codon usage prefers A/C at the third codon position and it was less towards T/G in its third codon position. The codons absent in pisces were AGT (except Toxotes chatareus), TGT, and CAG (except Elasma zonatum). The codons such as AGT (except Falco peregrinus), CGT (except Vidua chalybeata), and ACG (except Aythya americana) were absent in aves whereas, in mammals, the absent codons were namely CAG (except Canis familiaris) and ACG (except Rattus norvegicus). Codon usage bias was low in pisces, aves, and mammals. The frequency of leucine was the highest in the amino acid and cysteine was the lowest. Correlation analysis further suggests that mutation pressure is mainly responsible for codon usage pattern. Natural selection might also play a vital role in codon usage pattern but it was weaker than mutation pressure.
authors.affiliation: a Department of Biotechnology , Assam University , Silchar , Assam , India.
authors.forename: Arif
authors.initials: A
authors.lastname: Uddin
authors.affiliation: a Department of Biotechnology , Assam University , Silchar , Assam , India.
authors.forename: Supriyo
authors.initials: S
authors.lastname: Chakraborty
mesh_terms: D000818:Animals; D001482:Base Composition; D001717:Birds / Q000235:genetics / Q000378:metabolism; D003062:Codon; D045303:Cytochromes b / Q000235:genetics*; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics / Q000378:metabolism; D050259:Genes, Mitochondrial; D008322:Mammals / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D014714:Vertebrates / Q000235:genetics* / Q000378:metabolism
chemical_list: D003062:Codon; D045303:Cytochromes b
keywords: CYB gene; Codon usage; mutation pressure; natural selection