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.

In 17 deletion variants, the 5 0 end of the deletion extended into NIaPro; the frequencies of these variants in the virus populations range from 8.44 Â 10 À5 (positions 6538-8478; Lineage 4) to 1.73 Â 10 À3 (positions 6460-8478; Lineage 4). Furthermore, in eight other variants the deletion started within NIaPro (upmost 5 0 position being 6516) and ended within CP (downmost 3 0 position being 9163), varying in frequency from 1.02 Â 10 À4 (positions 6923-9013; Lineage 4) to 1.88Â10 À3 (positions 6569-8746; Lineage 1). The 43.75% of genotypes carrying deletions larger than the NIb cistron will produce viruses with truncated cistrons NIaPro, CP, or both. Moreover, deletions beyond the NIb cistron will lead to the loss of proteolytic cleavage sites and result in fusion of the truncated proteins. These genomes will probably be defective particles and some may additionally interfere with replication of the full-length virus. These defective particles can only replicate if they are complemented by a full-length TEV or possibly other defective genomes, and their spread may therefore be limited. The highest frequency of putatively defective deletion variants does not exceed 1%, in line with our expectations: two NIaPro-to-CP deletion variants (positions 6569-8746 and 6774-8795; Lineage 1) show frequencies of 1.88 Â 10 À3 and 1.58 Â 10 À3 , respectively. All lineages are dominated by variants with NIb deletion only, which is consistent with the fact that these variants are viable. Although defective viruses are often maintained in virus populations by complementation (Roux et al. 1991; Moreno et al. 1997; Froissart et al. 2004; García-Arriaza et al. 2004) , the low level of coinfection (Dietrich and Maiss 2003; Tromas et al. 2014 ) may rapidly eliminate defective viruses from potyvirus populations.