Characterization of a novel dsRNA endornavirus in the plant pathogenic fungus Thielaviopsis basicola

Abstract

Double-stranded (ds) RNA elements are commonly present in strains of the plant pathogenic fungus Thielaviopsis basicola which infects a wide range of plant species. To characterize a novel 12 kb dsRNA in strain NC1527 of this fungus, reverse transcription-polymerase chain reaction (RT-PCR) was used to obtain an 11,602 bp cDNA sequence from overlapping cDNA clones. Northern blot analysis confirmed that 15 individual cDNA clones that covered the entire length of the cDNA sequence all hybridized to the 12 kb dsRNA. An open reading frame (ORF) search revealed that the 5′non-coding region of this sequence spans 27 nucleotides, followed by one large ORF of 11,575 bp nucleotides, which potentially encodes a large putative polyprotein of 3858 amino acid residues. Specialized Basic Local Alignment Search Tool (BLAST) searches of conserved domains indicated that the putative polyprotein contained a viral RNA helicase1 (Hel), glycosyl transferase (GT) and RNA-dependent RNA polymerase (RdRp) domain regions. BLASTp searches in the protein database using translated nucleotides showed that the cloned dsRNA had homology to endornaviruses, which are present in a few fungi as well as some plant species. The amino acid homologies ranged from 28% to 34% in the RdRp domain region, 23–32% in the helicase domain region and 29–30% in GT region. We designate this dsRNA element as a new endornavirus, Chalara elegans endornavirus 1 (CeEV1). Phylogenetic comparison of the sequence of RdRP with other endornavirus indicated that CeEV1 was relatively distant and may be an ancestral form.