title: A novel RNA mycovirus in a hypovirulent isolate of the plant pathogen Diaporthe ambigua.
abstract: Hypovirulent isolates of the fruit tree fungal pathogen Diaporthe ambigua have previously been shown to harbour a double-stranded (ds)RNA genetic element of about 4 kb. In this study, we established the complete cDNA sequence of this dsRNA, which represents a replicative form of a positive-strand RNA virus that we have named D. ambigua RNA virus (DaRV). The nucleotide sequence of the genome is 4113 bp and has a GC content of 53%. Two large ORFs are present in the same reading frame. They are most probably translated by readthrough of a UAG stop codon in the central part of the genome. The longest possible translation product (p125) has a predicted molecular mass of about 125 kDa. A significant homology can be found to the non-structural proteins of carmoviruses of the positive-strand RNA virus family TOMBUSVIRIDAE: These proteins also include the conserved RNA-dependent RNA polymerase (RDRP) domain. In contrast to the genome organization of these plant viruses, no ORF is present at the 3' end of the DaRV genome that encodes a coat protein. Therefore, it is proposed that DaRV is not encapsidated but that it occurs as RNA-RDRP complexes and/or that it might be associated with cell membranes. Interestingly, six putative transmembrane helices are predicted in the N-terminal part of p56 (translation product of the first ORF, N-terminal part of p125), which might direct and anchor the viral complex to membranes. DaRV is a mycovirus with a unique genome organization and has a distant relationship to the plant virus family TOMBUSVIRIDAE:
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa1.
authors.forename: O
authors.initials: O
authors.lastname: Preisig
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa1.
authors.forename: N
authors.initials: N
authors.lastname: Moleleki
authors.affiliation: ARC-Fruit, Vine and Wine Research Institute, Private Bag X5013, Stellenbosch 7599, South Africa2.
authors.forename: W A
authors.initials: WA
authors.lastname: Smit
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa1.
authors.forename: B D
authors.initials: BD
authors.lastname: Wingfield
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa1.
authors.forename: M J
authors.initials: MJ
authors.lastname: Wingfield
mesh_terms: D000595:Amino Acid Sequence; D001203:Ascomycota / Q000472:pathogenicity* / Q000821:virology*; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000032:analysis / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D012328:RNA Viruses / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D012330:RNA, Double-Stranded / Q000032:analysis / Q000235:genetics; D012367:RNA, Viral / Q000032:analysis / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D019183:Tombusviridae / Q000737:chemistry / Q000235:genetics; D014197:Trees / Q000382:microbiology*; D014774:Virulence
chemical_list: D018076:DNA, Complementary; D012330:RNA, Double-Stranded; D012367:RNA, Viral