Genome-wide comparative analysis of the codon usage pattern in Flaviviridae family

Abstract

Flaviviridae family is a group of viruses that cause several deadly diseases like Dengue Fever Virus, Zika Virus, Japa-nese Encephalitis Virus, and Hepatitis C Virus etc. The codon usage analysis can serve as a tool to understand about the molecular evolution and regulation of viral gene expression. The objective of this study is to fi nd the key deter-minants of codon usage in the family. In this study, the codon usage pattern for 114 genomes of Flaviviridae family (with four genus Flavivirus, Hepacivirus, Pegivirus, Pestivirus) was analysed through codon usage indices (like NC, RSCU, ENC, PCA) and multivariate statistical methods. Our results show that among the four genus Flavivirus and Pestivirus show similarity in preferred base on the count of being AG rich. On the other hand, Pegivirus and Hepacivi-rus show similarity in preferred base on the count of being GC rich. The overall codon usage bias in the entire family is slightly biased. RSCU analysis showed that Flavivirus and Pestivirus prefer AG ending codons, whereas Pegivirus and Hepacivirus show preference to GC ending codons. Many unclassifi ed members show similarity with members of genus Flavivirus in choices of codon. The ENC -GC3 plot show that mutation pressure is dominating evolutionary driving force in making codon usage preferences. The study represents comprehensive analysis of codon usage pat-tern and help to better understand the mechanism of codon usage bias.