Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species

Wassenaar, Trudy M.; Jun, Se-Ran; Robeson, Michael; Ussery, David W.

Appendix Figure A1 compares the RSCU values of the three viral species, plotted in a wheel plot. This identified differences in codon usage between HAV on the one hand and HCV/HEV on the other hand. The codon usage of HAV is suboptimal for replication in the human host, while the codon usage of HCV is highly adapted to that of human cells, as has been described before (Pintó, Aragonès, Costafreda, Ribes, & Bosch, 2007) . RCSU values are an excellent means to compare codon usage of individual genes within a given (prokaryotic) genome, as cells typically control gene expression by minor codon preferences (Sharp & Li, 1986) . However, when comparing virus proteomes with large differences in codon usage, we consider it useful to look at this usage without correcting for nucleotide composition differences, as a dependence exists between nucleotide composition and codon usage preferences. Thus, we calculated codon usage as the fraction of used codons per given amino acid.