title: Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus.
abstract: Recently, several outbreaks of Japanese encephalitis (JE), caused by Japanese encephalitis virus (JEV), have been reported and it has become cause of concern across the world. In this study, detailed analysis of JEV codon usage pattern was performed. The relative synonymous codon usage (RSCU) values along with mean effective number of codons (ENC) value of 55.30 indicated the presence of low codon usages bias in JEV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations of A3s, U3s, G3s, C3s, GC3s, ENC values, with overall nucleotide contents (A%, U%, G%, C%, and GC%). The correlation analysis of A3s, U3s, G3s, C3s, GC3s, with axis values of correspondence analysis (CoA) further confirmed the role of mutational pressure. However, the correlation analysis of Gravy values and Aroma values with A3s, U3s, G3s, C3s, and GC3s, indicated the presence of natural selection on codon usage bias in addition to mutational pressure. The natural selection was further confirmed by codon adaptation index (CAI) analysis. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern to some extent.
authors.affiliation: School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India. Electronic address: nirajvet57@gmail.com.
authors.forename: Niraj K
authors.initials: NK
authors.lastname: Singh
authors.affiliation: College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India.
authors.forename: Anuj
authors.initials: A
authors.lastname: Tyagi
authors.affiliation: School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India.
authors.forename: Rajinder
authors.initials: R
authors.lastname: Kaur
authors.affiliation: School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India.
authors.forename: Ramneek
authors.initials: R
authors.lastname: Verma
authors.affiliation: Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar 243122, India.
authors.forename: Praveen K
authors.initials: PK
authors.lastname: Gupta
mesh_terms: D000220:Adaptation, Biological; D001482:Base Composition; D003062:Codon; D019295:Computational Biology; D004664:Encephalitis Virus, Japanese / Q000235:genetics*; D019143:Evolution, Molecular; D016679:Genome, Viral; D009154:Mutation; D009711:Nucleotides / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D003062:Codon; D009711:Nucleotides
keywords: Codon usage bias; Japanese encephalitis virus; Mutational pressure; Natural selection