Analysis of synonymous codon usage in spike protein gene of infectious bronchitis virus

Infectious bronchitis virus (IBV) is responsible for causing respiratory, renal and urogenital disease in poultry. IBV infection in poultry lead to high mortality rates in affected flocks and severe economic losses due to drop in egg production and reduce gain in live weight of the broiler birds. IBV encoded spike protein (S) is the major host protective immunogen. Although the functions of the S protein have been well studied, the factors shaping synonymous codon usage bias and nucleotide composition in the S gene have not been reported yet. In the present study, we have analyzed the relative synonymous codon usage and effective number of codons (ENC) using the 53 IBV S genes. The major trend in codon usage variation was studied using correspondence analysis. The plot of ENC values and GC3s as well as the correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in S gene. Interestingly, no association of aromaticity, degree of hydrophobicity and aliphatic index has been observed with the codon usage variation in IBV S genes. The study represents a comprehensive analysis of IBV S gene codon usage patterns and provides a basic understanding of the codon usage bias.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author