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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research » Research » Publications at this Location » Publication #307211

Research Project: Genetic Improvement and Virus Management of Small Fruit Crops

Location: Horticultural Crops Research

Title: A variant of Rubus yellow net virus with altered genomic organization

Author
item Diaz-lara, Alfredo - Oregon State University
item Mosier, Nola
item Keller, Karen
item Martin, Robert - Bob

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/20/2014
Publication Date: 12/6/2014
Citation: Diaz-Lara, A., Mosier, N.J., Keller, K.E., Martin, R.R. 2014. A variant of Rubus yellow net virus with altered genomic organization. Virus Genes. 50(1):104-110.

Interpretive Summary: We characterized a novel strain of Rubus yellow net virus obtained from the National Clonal Germplasm Repository, that likely originated in Europe. It has a nearly identical sequence (>99%) to the fragment of Rubus yellow net virus reported from Europe and is quite distinct from an isolate sequenced from North America. The large raspberry aphid from North America (Amphorophora agathonica) was able to acquire but not transmit this virus in laboratory and greenhouse studies, though the virus was graft transmissible. This lack of aphid transmission may be due to the absence of one protein or a truncated protein produced by this virus compared to the virus isolate sequenced from North America. Or the lack of transmission could be due to this virus being from Europe where it evolved with a different virus vector (Amphorophora idaeus). Further work on the variability of this virus within North America will shed light on the reason that this isolate was not transmitted by the raspberry aphid from North America.

Technical Abstract: Rubus yellow net virus (RYNV) is a member of the family Caulimoviridae, genus Badnavirus. RYNV infects Rubus species causing chlorosis of the tissue along the leaf veins, giving an unevenly distributed netted symptom in some cultivars of red and black raspberry. Recently, this virus was isolated and characterized from native R. strigosus plants in Alberta, Canada, exhibiting such symptoms. The viral genome contained seven open reading frames (ORF) with five of them in the sense-strand, including a large polyprotein. The isolate from Canada (RYNV-Ca) is the only complete sequence of RYNV available in GenBank. Here we describe a graft transmissible strain of RYNV from Europe infecting cultivar ‘Baumforth’s Seedling A’ (named RYNV-BS), which was sequenced using Rolling Circle Amplification (RCA), enzymatic digestion, cloning and primer walking, plus resequenced at a 5X coverage. This sequence was then compared with the RYNV-Ca genome and significant differences were observed. Genomic analysis identified differences in the arrangement of coding regions, promoter elements and presence of motifs. The genomic organization of RYNV-BS consisted of six ORFs (five ORFs in the sense-strand and one ORF in antisense-strand). ORFs 1, 2 and 3 showed a high degree of homology to RYNV-Ca, on the other hand, ORFs 4, 5 and 6 of RYNV-BS were quite distinct. Also, the predicted ORF 7 in the RYNV-Ca was absent in the RYNV-BS sequence. These differences may account for the lack of aphid transmissibility of RYNV-BS.