Comparison of the Nucleotide Sequences of Five Tomato Black Ring Virus Satellite RNAs

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Abstract
The nucleotide sequences of the satellite RNAs associated with tomato black ring virus isolates L, G, E and C were determined and compared with the sequence of the satellite associated with strain S determined earlier. The sequence of satellite L closely resembled that of satellite S and both were to a lesser extent similar to satellites G, E, and C which themselves were closely similar. There was 90% or more sequence homology between satellites in each group, G and E being the most closely related, with only one nucleotide (nt) difference between them. There was about 60% homology between the groups. Satellites G, E and C had longer 5'' non-coding regions (40 nt) than satellites L and S (14 nt), but were shorter by 11 to 13 nt in their 3'' non-coding regions. The sequences all contained a single large open reading frame for proteins of mol. wt. 47808 (424 amino acids) (L), 47792 (419 amino acids) (G, E) and 47698 (419 amino acids) (C). The deduced amino acid sequences differed principally in their N-terminal 65 residues. Several regions of sequence comprising 10 or more amino acids, and one of 31 amino acids, were identical in all satellite sequences. No marked sequence similarities were detected between the satellite sequences and a number of viral protein and nucleic acid sequences available in databases. The extent of homology between the 3'' ends of satellite sequences and those of RNA-1 or RNA-2 of TBRV was slight, consisting of several hexa- and heptanucleotides.