Polyadenylation and reverse transcription of bacteriophage phi 6 double-stranded RNA

A Rapid Method for Sequencing Double-Stranded RNAs Purified from Yeasts and the Identification of a Potent K1 Killer Toxin Isolated from Saccharomyces cerevisiae

Mycoviruses infect a large number of diverse fungal species, but considering their prevalence, relatively few high-quality genome sequences have been determined. Many mycoviruses have linear double-stranded RNA genomes, which makes it technically challenging to ascertain their nucleotide sequence using conventional sequencing methods. Different specialist methodologies have been developed for the extraction of double-stranded RNAs from fungi and the subsequent synthesis of cDNAs for cloning and sequencing. However, these methods are often labor-intensive, time-consuming, and can require several days to produce cDNAs from double-stranded RNAs. Here, we describe a comprehensive method for the rapid extraction and sequencing of dsRNAs derived from yeasts, using short-read next generation sequencing. This method optimizes the extraction of high-quality double-stranded RNAs from yeasts and 3′ polyadenylation for the initiation of cDNA synthesis for next-generation sequencing. We have used this method to determine the sequence of two mycoviruses and a double-stranded RNA satellite present within a single strain of the model yeast Saccharomyces cerevisiae. The quality and depth of coverage was sufficient to detect fixed and polymorphic mutations within viral populations extracted from a clonal yeast population. This method was also able to identify two fixed mutations within the alpha-domain of a variant K1 killer toxin encoded on a satellite double-stranded RNA. Relative to the canonical K1 toxin, these newly reported mutations increased the cytotoxicity of the K1 toxin against a specific species of yeast.

Synthesis of a double-stranded cDNA transcript of the killer toxin-coding region of the yeast M1 double-stranded RNA

Reverse transcription of methylmercuryhydroxide-treated M1 double-stranded RNA of yeast produces several discrete single-stranded and double-stranded cDNA's from oligo (dT)12-18 primer. S1 nuclease analysis shows that the longest transcript of the 1.8 kb template, a 2.2 kb molecule, is a 1.1 kb duplex terminated at one end by a hairpin-like structure. The 1.1 kb ds cDNA contains a complete copy of the M1-1, toxin-coding, sequence of M1 double-stranded RNA, and its synthesis is primed from oligo (dT)12-18 that anneals to a sequence within the internal, AU-rich, region of the template.