1 3 Analysis of codon usage pattern evolution in avian rotaviruses and their 4 preferred host 5 6 7 Jobin Jose Kattoor a , Yashpal Singh Malik a,⇑ , Aravind Sasidharan b , Vishnuraj Mangalathu Rajan a , 8 Kuldeep Dhama a , Souvik Ghosh c , Krisztián Bányai d , Nobumichi Kobayashi e , Raj Kumar Singh a 9 a Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India 10 b National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India 11 c 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 12 Kitts and Nevis 13 d Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary 14 e Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo, Japan 15 16 18 article info 19 Article history: 20 Received 28 February 2015 21 Received in revised form 26 May 2015 22 Accepted 14 June 2015 23 Available online xxxx 24 Keywords: 25 Avian rotavirus 26 VP6 gene 27 Relative synonymous codon usage 28 Effective number of codons 29 Codon adaptation index 30 Geographical separation 31 Virus evolution in host 32 33 abstract 34 Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 35 species (A–H). We report here the evolution assessment of codon usage patterns in virus–host system 36 in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleo- 37 tide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of 38 codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) 39 of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus 40 (RV) genetic diversity and impact of host’s natural selection on the AvRVs codons. Synonymous codon 41 usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding 42 gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topol- 43 ogy confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adap- 44 tation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon 45 preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, 46 codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. 47 The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which 48 could be exploited for additional research on avian species in future. 49 Ó 2015 Published by Elsevier B.V. 50 51 52 53 54 1. Introduction 55 The Codon Usage Bias (CUB) is an exclusive uniqueness of geno- 56 mic sequences encoding proteins (Hershberg and Petrov, 2008). 57 Hitherto studies proved that certain genes display defined prefer- 58 ence for certain codons for the same amino acid, rather using the 59 available codons randomly. The changes at 3rd codon’s GC%s and 60 synonymous codons in coding DNA, are the most apparent crite- 61 rion in codon usage evolution which possibly lead to noticeable 62 CUB (Shackelton et al., 2006; Yang and Nielsen, 2008), making 63 them a mark for studying virus–host evolution. Furthermore, the 64 compositional limits, translational selection (Ghosh et al., 2000) 65 and mutational forces (Jenkins and Holmes, 2003) are other iden- 66 tified factors observed making significant part in the relative syn- 67 onymous codon usage pattern. The redundancy of genetic code 68 and synonymous codon usage offers the organism an opportunity 69 to focus on efficient protein synthesis and folding (Ikemura, 70 1982) and possessing the analogous amino acid sequence 71 (Stoletzki and Eyre-Walker, 2007). It has been found that, in unicel- 72 lular organisms like Escherichia coli and Bacillus subtilis, highly 73 expressed genes have high preferential usage of certain codons 74 with matching tRNA (Sharp and Li, 1986), although lesser http://dx.doi.org/10.1016/j.meegid.2015.06.018 1567-1348/Ó 2015 Published by Elsevier B.V. Abbreviations: VP, viral protein; AvRV, avian rotavirus; RVA, rotavirus species A; RVD, rotavirus species D; RVF, rotavirus species F; RVG, rotavirus species G; ORF, open reading frame; CAI, codon adaptation index; CoA, correspondence analysis; ENc, effective number of codons; RSCU, relative synonymous codon usage values; GC 3 , the frequencies of nucleotide G + C at third codon position. ⇑ Corresponding author. E-mail addresses: jobinjkattoor@gmail.com (J.J. Kattoor), malikys@ivri.res.in (Y.S. Malik), aravindspillai02@gmail.com (A. Sasidharan), vishnurajmr@gmail.com (V.M. Rajan), dhamak@rediffmail.com (K. Dhama), souvikrota@gmail.com (S. Ghosh), bkrota@hotmail.com (K. Bányai), koba103161@yahoo.co.jp (N. Kobayashi), rks_virology@rediffmail.com (R.K. Singh). Infection, Genetics and Evolution xxx (2015) xxx–xxx Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid MEEGID 2382 No. of Pages 9, Model 5G 16 June 2015 Please cite this article in press as: Kattoor, J.J., et al. Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host. Infect. Genet. Evol. (2015), http://dx.doi.org/10.1016/j.meegid.2015.06.018