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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
An umbra-related virus found in babaco (Vasconcellea × heilbornii)
Juan F Cornejo-Franco1, Francisco Flores2,3, Dimitre Mollov4
1Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador.
Abstract:
The complete sequence of a new viral RNA from babaco (Vasconcellea × heilbornii) was determined. The genome consisted of 4,584 nucleotides, containing two open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5' terminus, and an unusually long (1,843 nt) NCR at the 3' terminus. The presence of a potential heptameric slippery signal located 12 nt upstream the stop codon of ORF 1 suggests a -1 ribosomal frameshift mechanism for the translation of ORF 2. Sequence comparisons of ORF 2 revealed similarity to the RNA-dependent RNA polymerase (RdRp) of several umbra- and umbra-like viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported in papaya, citrus, opuntia, maize, and sugarcane hosts. Viruses of this clade share a most recent ancestor with the umbraviruses but have different genomic features. The creation of a new genus within the family Tombusviridae is proposed for the classification of these novel viruses.
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