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.

Our results provide further support for the notion of a relationship between genome size and replication/withinhost competitive fitness (Sakai et al. 1999; Marks et al. 2005; Zwart et al. 2010 Zwart et al. , 2014 , although there are clearly limitations to this idea (Bull et al. 2004) . Not only could TEV-ÁNIb outcompete TEV in transgenic plants, also all independent TEV lineages accumulate various NIb deletions upon passaging. We identified 64 different deletion variants, most of which conserved the reading frame. In 17 deletion variants the deletion extended far into the upstream cistron, NIaPro, while for eight deletion variants, the deletion also extended into the downstream cistron, CP. Because both NIaPro and CP proteins are essential for virus replication and these deletions removed one or more proteolytic cleavage sites, the virus variants probably cannot replicate autonomously, even in the transgenic plants. Therefore, the virus population in the simulated NIRV-expressing host appears to have generated two types of defective viruses: 1) those with deletions in NIb only and can replicate autonomously in the transgenic plants but not in the wild-type plants and 2) those with deletions extending beyond the NIb cistron, which cannot replicate autonomously in either host. On the basis of these observations, we speculate that the NIRV-expressing hosts may be a source of defective genotypes in natural virus populations. If a deletion genotype arises de novo in a NIRV-expressing host, it will not require coinfection with a full-length virus to be maintained in the population. Consequently, it may more easily reach intermediate to high frequencies in a NIRV-expressing plant, allowing the defective virus to be sustained even in non-NIRV hosts by coinfection with full-length viruses (Montville et al. 2005) . Complementation can slow down the rate at which deleterious alleles are eliminated from the virus population (Froissart et al. 2004 ; Sardanyé s and Elena 2010) and promote selection for defective-interfering particles as cheater genotypes that reduce mean population fitness (Turner and Chao 1999) .