title: Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host.
abstract: Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A-H). We report here the evolution assessment of codon usage patterns in virus-host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host's natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future.
authors.affiliation: Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India. Electronic address: jobinjkattoor@gmail.com.
authors.forename: Jobin Jose
authors.initials: JJ
authors.lastname: Kattoor
authors.affiliation: Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India. Electronic address: malikys@ivri.res.in.
authors.forename: Yashpal Singh
authors.initials: YS
authors.lastname: Malik
authors.affiliation: National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India. Electronic address: aravindspillai02@gmail.com.
authors.forename: Aravind
authors.initials: A
authors.lastname: Sasidharan
authors.affiliation: Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India. Electronic address: vishnurajmr@gmail.com.
authors.forename: Vishnuraj Mangalathu
authors.initials: VM
authors.lastname: Rajan
authors.affiliation: Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India. Electronic address: dhamak@rediffmail.com.
authors.forename: Kuldeep
authors.initials: K
authors.lastname: Dhama
authors.affiliation: Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P. O. Box 334, Basseterre, Saint Kitts and Nevis. Electronic address: souvikrota@gmail.com.
authors.forename: Souvik
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary. Electronic address: bkrota@hotmail.com.
authors.forename: Krisztián
authors.initials: K
authors.lastname: Bányai
authors.affiliation: Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo, Japan. Electronic address: koba103161@yahoo.co.jp.
authors.forename: Nobumichi
authors.initials: N
authors.lastname: Kobayashi
authors.affiliation: Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India. Electronic address: rks_virology@rediffmail.com.
authors.forename: Raj Kumar
authors.initials: RK
authors.lastname: Singh
mesh_terms: D000818:Animals; D000956:Antigens, Viral / Q000235:genetics; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics; D002645:Chickens / Q000821:virology*; D003062:Codon; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D058507:Host Specificity; D054884:Host-Pathogen Interactions; D011201:Poultry Diseases / Q000821:virology*; D012401:Rotavirus / Q000235:genetics*; D012400:Rotavirus Infections / Q000662:veterinary* / Q000821:virology
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D003062:Codon; C061332:VP6 protein, Rotavirus
keywords: Avian rotavirus; Codon adaptation index; Effective number of codons; Geographical separation; Relative synonymous codon usage; VP6 gene; Virus evolution in host