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.

All evolved lineages of TEV and TEV-ÁNIb were fully sequenced to determine whether there were differences in their patterns of molecular evolution. We were particularly interested in understanding whether the use of NIb in trans may have affected the regulation of expression and accumulation of all other viral components. Mutational spectra for both viral genotypes were dominated by point mutations as not a single insertion or deletion was observed (table 2). As anticipated, the passaging setup used leads to the retention of NIb cistron by all TEV lineages, and by contrasting the evolution of TEV and TEV-ÁNIb, we are therefore considering the evolutionary effects of having a full-length or truncated genome. There were no differences between ratios of transitions to transversions; the ratio was 8.5 for TEV and 6.0 for TEV-DNIb (Fisher's exact test: P ¼ 1.000). Given that it is biochemically easier to produce transitions than transversions, it is not surprising to observe these biased ratios. Likewise, there was not a significant difference in the ratio of synonymous to nonsynonymous substitutions between the two viruses (Fisher's exact test: P ¼ 0.330); for TEV, this ratio was 1.375 whereas for TEV-DNIb it was 0.636. For both genotypes, mutations were evenly distributed along the genome ( fig. 4A ; Kolgomorov-Smirnov test: TEV n ¼ 19, P ¼ 0.330; TEV-ÁNIb n ¼ 21, P ¼ 0.688). An interesting example of convergent evolution was mutation A6805G (K2269E) that appeared in 80% of TEV lineages and in 40% of TEV-ÁNIb lineages. This nonsynonymous mutation is localized in a superficial domain of NIaPro (Nunn et al. 2005) , and it could affect the proteinase function or modulate the interactions of NIaPro with other proteins. This same mutation has also been previously reported in serial-passage evolution experiments of TEV in N. tabacum: in 10% of lineages after 15 one-week passages (Bedhomme et al. 2012) , and in 30% of lineages after three 9-week passages ).