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United States Department of Agriculture

Agricultural Research Service

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

Location: Horticultural Crops Research

Title: A Raspberry bushy dwarf virus isolate from Ecuadorean Rubus glaucus contains an additional RNA that is a rearrangement of RNA 2

Authors
item Quito-Avila, D -
item Peralta, E -
item Ibarra, M -
item Alvarez, R -
item Martin, Robert

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 10, 2014
Publication Date: April 10, 2014
Citation: Quito-Avila, D.F., Peralta, E.L., Ibarra, M.A., Alvarez, R., Martin, R.R. 2014. A Raspberry bushy dwarf virus isolate from Ecuadorean Rubus glaucus contains an additional RNA that is a rearrangement of RNA 2. Archives of Virology. DOI: 10.1007/s00705-014-2069-4.

Interpretive Summary: A new of Raspberry bushy dwarf virus isolate was identified in commercial blackberry (Rubus glaucus) in Azuay, province of Ecuador and named RBDV-Ec-Az. The virus contains an extra RNA compared to all other RBDV isolates that have been sequenced. This extra RNA contains a complete copy of RNA 2, plus an extra copy of the coat protein in reverse order at the 5' end of the RNA. This is a unique duplication among plant viruses and its significance is still being evaluated. The extra RNA was present in approximately 40% of the isolates from Azuay province, but it was not detected in Tungurahua province, which is the main blackberry production region for Ecuador. The ends of RNA 2 of this strain of RBDV was similar to the resistance breaking strain reported from the UK, while the portion of RNA2 that codes for proteins was more similar to RBDV is, was more similar isolates from Slovenia. It appears this strain of RBDV is a combination of several different strains of RBDV. This is also the first report of a complete sequence of RBDV from South America.

Technical Abstract: A new Raspberry bushy dwarf virus isolate was found in commercial blackberry (Rubus glaucus) in Azuay, province of Ecuador and named RBDV-Ec-Az. The complete bipartite genome was sequenced using dsRNA as initial template. RNA 1 was 5449 nucleotides (nt) long and the normal RBDV RNA 2 was 2231 nt long. Interestingly, an additional dsRNA band of about 3 kbp was observed in the dsRNA gels. Upon sequencing this band, it was 3279 bp long. Blast searches revealed that the segment was a modified version of RNA 2, which consisted of the 2231 nt corresponding to RNA 2 plus an additional 1048 nt fragment that was concatenated in a reverse-complemented fashion to its 5’ terminus. Analysis of the terminal sequences revealed that both, the normal (2231 nt) and the modified RNA 2 (3279 nt) were present in the same plant. Sequence analysis using the coat protein gene showed that the RBDV-Ec-Az shares 99% nucleotide identity with RBDV isolate RR-1 from red raspberry in Slovenia. However, RBDV-Ec-Az possesses the exact terminal sequences as those found in the resistance breaking strain R-15 from European ‘Malling Jewel’ red raspberry. This communication reports for the first time an unusual viral genomic RNA with a 1048 nt long concatenated sequence and provides the first record of the complete genomic sequence of an RBDV isolate from R. glaucus in South America.

Last Modified: 12/21/2014
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