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Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved 3'-terminal structures among members of the genus Crinivirus

I. C. Livieratos^1,

E. Eliasco^1,

¹ Department of Biological Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK
² The International Potato Center, Apartado 1558, Lima, Peru
³ Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands

Correspondence
R. H. A. Coutts
r.coutts{at}imperial.ac.uk

Double-stranded RNA preparations produced from potato plants graft-inoculated with a Peruvian isolate of Potato yellow vein virus (PYVV; genus Crinivirus, family Closteroviridae) contain five RNA species denoted RNA 1, RNA 2, RNA 3, x and y of approximately 8, 5·3, 3·8, 2·0 and 1·8 kbp, respectively. The complete nucleotide sequences of PYVV RNAs 1, 2 and 3 and Northern hybridization analysis showed that PYVV RNA 1 contained the replication module and an additional open reading frame (p7), while two distinct species, RNAs 2 and 3, contain the Closteroviridae hallmark gene array. Pairwise comparisons and phylogeny of genome-encoded proteins showed that PYVV shares significant homology with other criniviruses but is most closely related to the Trialeurodes vaporariorum-vectored Cucumber yellows virus. Secondary structure prediction of the 3'-untranslated regions of all three PYVV RNAs revealed four conserved stem–loop structures and a 3'-terminal pseudoknot structure, also predicted for all fully characterized members of the genus Crinivirus and some members of the genera Closterovirus and Ampelovirus.

The GenBank accession numbers for the nucleotide sequences determined in this work are AJ557128 (RNA 1), AJ557129 (RNA 2) and AJ508757 (RNA 3).

Both authors contributed equally to this work.