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

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Abstract
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, 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.