Complementary DNAs corresponding to the virion RNAs of the ST9 isolate of beet western yellows virus (ST9 BWYV) were cloned and the complete, 2843 nucleotide sequence of a unique RNA associated with ST9 BWYV, the ST9-associated RNA (ST9 aRNA), was determined. Three ORFs with deduced translation products of molecular weights 22,600, 12,500, and 35,900, respectively, and a small ORF, potentially encoding for a 3400 molecular weight protein, were identified in the ST9 aRNA sequence. Possible gene products of the ST9 aRNA were identified by in vitro translation analysis of the ST9 BWYV virion RNAs (the ST9 BWYV genomic RNA [ST9 BWYV gRNA] and the ST9 aRNA) and of transcripts representing the nearly full-length ST9 aRNA, individual ORFs, and specific ORF combinations. Proteins of 23,000 and 28,000 M(r) were derived from ORF 1 transcripts, while proteins of 25,000 and 35,000 M(r) were derived from ORF 3 transcripts. Larger proteins of 85,000 and 45,000 M(r) were also identified, and shown to possibly arise by continuous translation of ORFs 1, 2, and 3 (by possible readthrough and frameshift), or ORFs 2 and 3 (by possible frameshift), respectively. No products were detected from transcripts representing only ORF 2. Computer database searches and analyses indicated that the ST9 aRNA shares significant nucleotide sequence homology with carmo-like viruses, but not with its helper virus, BWYV. Amino acid sequence analyses also indicated that the ST9 aRNA ORF 2 and ORF 3 regions share extensive homology with putative RNA-dependent RNA polymerases of carmo-like viruses.