title: A variant of Rubus yellow net virus with altered genomic organization.
abstract: Rubus yellow net virus (RYNV) is a member of the genus Badnavirus (family: Caulimoviridae). 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, a strain of RYNV was sequenced from a Rubus idaeus plant in Alberta, Canada, exhibiting such symptoms. The viral genome contained seven open reading frames (ORFs) with five of them in the sense-strand, including a large polyprotein. 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, enzymatic digestion, cloning and primer walking, and it was 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 five ORFs (four ORFs in the sense-strand and one ORF in the antisense-strand). ORFs 1, 2, and 3 showed a high degree of homology to RYNV-Ca, while ORFs 4 and 6 of RYNV-BS were quite distinct. Also, the predicted ORFs 5 and 7 in the RYNV-Ca were absent in the RYNV-BS sequence. These differences may account for the lack of aphid transmissibility of RYNV-BS.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA, diazlara@onid.orst.edu.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Diaz-Lara
authors.forename: Nola J
authors.initials: NJ
authors.lastname: Mosier
authors.forename: Karen E
authors.initials: KE
authors.lastname: Keller
authors.forename: Robert R
authors.initials: RR
authors.lastname: Martin
mesh_terms: D019195:Badnavirus / Q000235:genetics* / Q000302:isolation & purification*; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D005060:Europe; D023061:Gene Order; D005814:Genes, Viral; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D011401:Promoter Regions, Genetic; D065856:Rubus / Q000821:virology; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D004279:DNA, Viral