RNA recombination in the genome of Barley stripe mosaic virus

Abstract Barley stripe mosaic Hordeivirus (BSMV) is a positive-strand RNA virus requiring three single-stranded RNAs (α, β, and γ) for infectivity. A terminal-sequence-dependent cloning strategy was used to clone the entire genome of the CV17 strain. Full-length γ cDNA clones were obtained when oligonucleotides specific for the 5′-terminal sequence of RNA α were used in the cloning procedure, but not when RNA γ-specific oligonucleotides were used. Sequence analysis of six putative γ cDNA clones revealed that nucleotides 1–70 possess 89% homology with the first 70 nucleotides of RNA α. This leader region is separated from the γ-specific coding region by an eight-base intervening sequence common to both CV17 RNAs α and γ. Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. Thus, the evidence suggests that RNA γ of BSMV strain CV17 is a recombinant molecule which may have arisen as a result of natural recombination between RNAs α and γ.