Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus

Sequences were recently obtained from four double-stranded (ds) RNAs from d ifferent plant species. These dsRNAs are not associated with particles and as they appeared not to be horizontally transmitted, they were thought to b e a kind of RNA plasmid, Here we report that the RNA-dependent RNA polymera se (RdRp) and helicase domains encoded by these dsRNAs are related to those of viruses of the alpha-like virus supergroup. Recent work on the RdRp seq uences of alpha-like viruses raised doubts about their relatedness, but our analyses confirm that almost all the viruses previously assigned to the su pergroup are related, Alpha-like viruses have single-stranded (ss) RNA geno mes and produce particles, and they are much more diverse than the dsRNAs. This difference in diversity suggests the ssRNA alpha-like virus form is ol der, and we speculate that the transformation to a dsRNA form began when an ancestral ssRNA virus lost its virion protein gene. The phylogeny of the d sRNAs indicates this transformation was not recent and features of the dsRN A genome structure and translation strategy suggest it is now irreversible. Our analyses also show some dsRNAs from distantly related plants are close ly related, indicating they have not strictly co-speciated with their hosts . In view of the affinities of the dsRNAs, we believe they should be classi fied as viruses and we suggest they be recognized as members of a new virus genus (Endornavirus) and family (Endoviridae).