Complete nucleotide sequence of a new satellite RNA associated with cucumber mosaic virus inducing tomato necrosis

A new strain (TN strain) of cucumber mosaic virus (CMV) was isolated from tomato plants with necrotic symptoms and proved to carry a necrogenic satellite RNA (TN-Sat RNA). Double-strand cDNA of the TN-Sat RNA was synthesized by reverse transcription and polymerase chain reaction using primers designed according to the conserved terminal sequences of known CMV satellite RNAs. Sequence analysis indicated that the TN-Sat RNA consisted of 390 nucleotides (nt). Comparison of the sequence of the TN-Sat RNA with those of other CMV satellite RNAs revealed four homologous regions (I. 1-81 nt; II. 216-261 nt; III. 278-338 nt; IV. 349-390 nt) and one hypervarible domain in the region of 82-215 nt. Moreover, the TN-Sat RNA contained a characteristic necrogenic consensus sequence at the 3' end (339-367 nt) as reported in the known necrosis-inducing CMV satellite RNAs.