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.

TEV-DNIb has a 16% smaller genome than TEV. If 1) a relationship between genome size and virus replication exists (Sakai et al. 1999; Zwart et al. 2014) and 2) dependence on in trans NIb expression for replication does not impose a large fitness burden to the virus, then NIb deletion in the virus genome will cause a faster replication and a selective advantage over a full-length wild-type virus. We therefore inoculated 15 N. tabacum 35S::NIb plants with a 1:1 mixture of ground infectious tissue with TEV and TEV-DNIb and measured the ratio of the two variants at 7, 21, and 63 dpi using quantitative reverse transcription PCR (RT-qPCR). Five plants were analyzed for each time point, meaning that each data point represents an independent measurement. On the basis of these data, we estimated the selective advantage for TEV as the per day selection rate constant W (Materials and Methods). A significant, upward-sloping linear regression was observed between time and the ratio of the TEV-DNIb:TEV ( fig. 1 ; r 2 ¼ 0.632, F 1,14 ¼ 22.330, P < 0.001), meaning that the ratio of the viruses shifts significantly toward TEV-ÁNIb, and this virus therefore has a significantly higher competitive fitness. We estimated that W ¼ 1.028 þ 0.006 d À1 (þ1 SD), suggesting that TEV-DNIb will slowly displace the wild-type virus in transgenic plants. If genome size was inversely proportional to fitness and the 16% reduction in genome size were the only determinant of fitness for TEV-DNIb, we would expect