Shrinkage of Genome Size in a Plant RNA Virus upon Transfer of an Essential Viral Gene into the Host Genome

Tromas, Nicolas; Zwart, Mark P.; Forment, Javier; Elena, Santiago F.

Here, we evaluated the patterns of genomic evolution of Tobacco etch virus (TEV, genus Potyvirus, family Potyviridae) in transgenic Nicotiana tabacum plants expressing NIb, the TEV RdRp (Li and Carrington 1995) . This system is an experimental model for exploring what the effects of high levels of NIRV expression are on virus infection and evolution. During infection of these transgenic plants, plant-derived NIb expression makes virus-derived NIb-expression redundant (Li and Carrington 1995) . We therefore expect that there may be relaxed selection for maintenance of the NIb cistron in the viral genome, which might lead to selection of variants with genomic deletions at the NIb locus, due to the replicative advantage associated with a smaller genome size. Ultimately, the expression of NIb might therefore induce genome shrinkage and result in a virus population that can no longer autonomously infect wild-type plants. We first determined whether the deletion of viral NIb led to an increase in viral fitness in NIbexpressing plants. Then, we passaged a full-length wild-type virus in NIb-expressing plants and used next-generation sequencing (NGS) to check for deletions in TEV NIb locus. Finally, we preempted the complete deletion of TEV NIb in NIb-expressing plants and studied the effects of NIb complementation in trans on genomic changes.