Adaption of tobacco rattle virus to its solanaceous hosts is related to the codon usage bias of the hosts and that of the viral 16 K gene

Tobacco rattle virus (TRV) is a member of the genus Tobravirus , family Virgaviridae , that infects many different plants from 50 families. TRV-based VIGS vectors are widely used in research into the interaction between viruses and their hosts in numerous plant species, especially those in the family Solanaceae . However, there is little known about the codon bias of solanaceous plants and that of TRV. In a comprehensive codon bias analysis of three plants ( Capsicum annuum , Solanum lycopersicum and S. tuberosum ), their optimal codons were identified and codon usage bias was shown to result from natural selection / mutation. Comparisons of relative codon deoptimization index (RCDI) and codon adaptation index (CAI) of TRV genes suggested that TRV may be better adapted to C. annuum than to S. lycopersicum and S. tuberosum . The average CAI of the 16 K gene, which is the RNA silencing suppressor of TRV, was higher than that of the other three genes in all three hosts, suggesting that the 16 K might be important for viral adaption to different solanaceous hosts. In a transient expression assay in leaves of Nicotiana benthamiana , a GFP-tagged clone of the TRV 16 K with deoptimized codon was expressed significantly less than a wild type sequence of TRV 16 K providing evidence that the virus-encoding silencing suppressor is significantly adapted to the codon usage bias of its hosts.