SEQUENCE-ANALYSIS OF THE TRAILER REGION OF SONCHUS YELLOW NET VIRUS GENOMIC RNA

The sequence of the 5' terminus (or the ''trailer'' region) of the min us-sense RNA genome of sonchus yellow net virus (SYNV) was determined by dideoxynucleotide termination sequencing of purified viral RNA and cloned cDNAs. The 5'-terminal nucleotide was identified by nuclease P1 digestion of P-32-end-laheled genomic RNA followed by polyethyleneimi ne cellulose chromatography. The trailer sequence occupies positions 1 3,561 to 13,720 relative to the 3' end of the genomic RNA and is compo sed of 160 nucleotides (nt) adjacent to a dinucleotide forming a porti on of the ''gene junction'' sequence at the terminus of the L protein gene. The trailer sequence is longer than the 144-nt plus-strand leade r RNA transcribed from the 3' end of the genomic RNA and is the longes t trailer sequence yet reported among the nonsegmented negative-strand viruses. As is characteristic of other rhabdovirus genomes, the 3' an d 5' termini of the SYNV genome are complementary and are capable of f orming a panhandle structure involving 16 of the 18 terminal nucleotid es, However, there is no obvious direct nucleotide sequence relatednes s between the SYNV trailer sequence and those of animal rhabdoviruses and paramyxoviruses. The existence of a minus-strand leader RNA of the same polarity as the trailer sequence could not be detected in nuclei c acid extracted from infected plants under hybridization conditions s uitable for detection of the plus-strand leader RNA, In this regard, S YNV differs from vesicular stomatitis virus and is similar to other rh abdoviruses which also fail to accumulate detectable minus-strand lead er RNAs. (C) 1994 Academic Press, Inc.