Suppressors of RNAi from plant viruses are subject to episodic positive selection

• Published in: Proceedings of the Royal Society. B, Biological sciences Vol. 280; no. 1765; p. 20130965
• Main Authors: Murray, Gemma G. R., Kosakovsky Pond, Sergei L., Obbard, Darren J.
• Format: Journal Article
• Language: English
• Published: England The Royal Society 22.08.2013
• Subjects: Animals; Antiviral Agents - metabolism; Antiviral Agents - pharmacology; Drosophila; Evolution, Molecular; Evolutionary Arms Race; Molecular Evolution; Phylogeny; Plant Viruses - classification; Plant Viruses - genetics; Plant Viruses - metabolism; Positive Selection; RNA interference; RNA Interference - drug effects; RNA silencing suppressors; RNA Viruses - classification; RNA Viruses - genetics; RNA Viruses - metabolism; Selection, Genetic; Viral Proteins - genetics; Viral Proteins - metabolism; Viral Proteins - pharmacology; Viral Suppressor Of Rnai; positive selection; RNA interference; viral suppressor of RNAi; evolutionary arms race; molecular evolution; RNA silencing suppressors
• ISSN: 0962-8452; 1471-2954; 1471-2945; 1471-2954
• DOI: 10.1098/rspb.2013.0965

Viral suppressors of RNAi (VSRs) are proteins that actively inhibit the antiviral RNA interference (RNAi) immune response, providing an immune evasion route for viruses. It has been hypothesized that VSRs are engaged in a molecular ‘arms race’ with RNAi pathway genes. Two lines of evidence support this. First, VSRs from plant viruses display high sequence diversity, and are frequently gained and lost over evolutionary time scales. Second, Drosophila antiviral RNAi genes show high rates of adaptive evolution. Here, we investigate whether VSRs diversify faster than other genes and, if so, whether this is a result of positive selection, as might be expected in an arms race. By analysis of 12 plant RNA viruses, we show that the relative rate of protein evolution is higher for VSRs than for other genes, but that this is not attributable to pervasive positive selection. We argue that, because evolutionary time scales are extremely different for viruses and eukaryotes, it is improbable that viral adaptation (as measured by the ratio of non-synonymous to synonymous change) will be dominated by one-to-one coevolution with eukaryotes. Instead, for plant virus VSRs, we find strong evidence of episodic selection—diversifying selection that acts on a subset of lineages—which might be attributable to frequent shifts between different host genotypes or species.