Wild-type and mutant double-stranded RNA (dsRNA) species from the yeast Saccharomyces cerevisiae were studied by electron microscopic heteroduplex mapping to determine the sequence relationships among the different RNA molecules. Three mutant dsRNAs, 1.5, 1.4, and 0.73 kilobase, were found to be derived by the same internal deletion of the wild-type (1.83 kilobases) molecule. This deletion includes a segment of about 200 base pairs that was estimated to be nearly 100% A + U. In addition, the sequences of the two larger mutant RNA species are tandem, direct duplications. One of the duplicated molecules appears to have a second internal deletion that occurred after the duplication. The mutant dsRNAs are functionally similar to the defective interfering virus particles of anima viruses all of the mutant species prevent the propagation of the wild-type dsRNA when both are present in the same cell. The four dsRNAs share the same sequences at their termini, a finding that may suggest that these sequences are important for the replication of the dsRNAs.Viruses and virus-like particles containing double-stranded RNA (dsRNA) are common to many species of fungi (1). Killer strains of the yeast Saccharomyces cerevisiae possess viral particles with two separately encapsidated dsRNA species: large (L), 2.5 X 106 daltons; and medium (M), 1.18 X 106 daltons (see refs. 2 and 3 for recent reviews). These strains excrete a toxic protein that kills sensitive strains but not killer strains. The M-dsRNA was believed to produce toxin and immunity to toxin because (i) the non-Mendelian segregation of these two killer traits is paralleled by cytoplasmic transmission of the dsRNA, and (ii) strains with an alteration in either toxin production or immunity either lack the M-dsRNA or have an altered form of it (4, 5). Recently, in vitro translation experiments have proved that M encodes the killer toxin (J. Hopper, personal communication). Denatured M-dsRNA directed the synthesis of a protein that, although larger than killer toxin, crossreacted with antiserumto toxin and contained all of the tryptic peptides of toxin produced in vivo. In similar in vitro experiments, the L-dsRNA directed the synthesis of the major capsid protein of the virus-like particles (6).Nonkiller mutants have been isolated that lack the M-dsRNA but have smaller (S) dsRNA species (7). When these mutants are mated to a killer strain the S-dsRNAs prevent or "suppress" the propagation of the M-dsRNA in the resulting diploids. With continued growth, the diploid cells rapidly become nonkillers and the M-dsRNA can no longer be detected. These suppressive S-dsRNAs therefore, are analogous to defective interfering virus particles, the subgenomic nucleic acid species of animal viruses that limit the replication of the standard virus during co-infection (8).This report describes electron microscopic heteroduplex mapping experiments between the M-and S-dsRNAs. The 4224 heteroduplexes studied show that the S-dsRNAs arose by deletions of M-dsRNA sequences. The various S-...