Arch Virol (1998) 143: 1535–1544
Nucleotide sequence of both genomic RNAs of a North American
tobacco rattle virus isolate
M. R. Sudarshana
and P. H. Berger
Division of Plant Pathology, Department of Plant, Soil and Entomological Sciences,
University of Idaho, Moscow, Idaho, U.S.A.
Accepted March 21, 1998
Summary. The complete sequence of a North American tobacco rattle virus
(TRV) isolate, ‘Oregon yellow’ (ORY), was determined from cDNA and RT-
PCR clones derived from the two genomic RNAs of this isolate. The RNA-1 is
6790 bases and RNA-2 is 3261 bases. The sequence of TRV-ORY RNA-1 was
similar to RNA-1 of TRV isolate SYM, and differs in 48 nucleotides. TRV-ORY
RNA-1 was one base shorter than -SYM, and had 47 base substitutions resulting
in 12 amino acid substitutions of which 4 were conservative. The RNA-2 of TRV-
ORY was distinct from RNA-2 of other characterized TRV isolates and contained
three open reading frames (ORFs) that could potentially code for proteins of MW
22.4 kDa, 37.6 kDa and 17.9 kDa. Based on the homology of the predicted amino
acid sequence with those of other tobraviruses, ORF1 of RNA-2 encodes the coat
protein (CP). The protein sequence of ORF2 had regions of limited similarity
with those of ORF2 of two other TRV isolates and pea early browning tobravirus.
The ORF3 was unique to TRV-ORY. Phylogenetic analysis of tobravirus CPs
indicated that TRV-ORY was most closely related to pepper ringspot tobravirus
and TRV-TCM. The relationship of tobravirus CPs to other rod-shaped tubular
plant viruses is also discussed.
In the US, TRV infection was reported in several crops [1, 4, 8, 30] and weeds
[6,18] and in most cases the isolates were only partially characterized. Most plant
The sequences reported in this paper have been deposited in the GenBank nucleotide
sequence database as accession numbers AF034621 and AF034622.
Present address: Department of Plant Pathology, University of California, Davis, CA