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Comparison of the Nucleotide Sequences of Viroid-like Satellite RNA of the Canadian and Australasian Strains of Lucerne Transient Streak Virus

¹ Department of Botany, University of Toronto, Toronto, Ontario M5S 1A1
and² Plant Research Centre, Agriculture Canada, Ottawa, Ontario K1A 0C6, Canada

A complete cDNA copy of the viroid-like satellite RNA of the Canadian strain of lucerne transient streak virus (LTSV) has been cloned and the nucleotide sequence of the RNA has been determined using this and other clones. The sequence comprises 322 residues and shares 80% homology with satellite RNAs (stRNAs) of the Australasian isolates of LTSV. A proposed secondary structure for the RNA is highly base-paired and thermodynamically stable, and consists of a rod-like structure interspersed with single-stranded loops, an arrangement similar to that proposed for circular stRNA of other strains of LTSV and other sobemoviruses as well as for viroids. Whereas certain regions of the sequence are very similar or identical to those of stRNA from Australasian LTSV, including the putative self-cleavage sites on both the positive and negative sense forms of the RNA, other regions of the sequence are quite dissimilar between the Canadian and Australasian strains.

Keywords: LTSV, nucleotide sequences, satellite RNA

Received 9 March 1988; accepted 25 May 1988.