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

A complete c D N A copy of the viroid-like satellite R N A of the Canadian strain of lucerne transient streak virus (LTSV) has been cloned and the nucleotide sequence of the R N A has been determined using this and other clones. The sequence comprises 322 residues and shares 8 0 ~ homology with satellite R N A s (s tRNAs) of the Australasian isolates of LTSV. A proposed secondary structure for the R N A is highly base-paired and thermodynamical ly stable, and consists of a rod-like structure interspersed with single-stranded loops, an arrangement similar to that proposed for circular s t R N A 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 s t R N A from Australasian LTSV, including the putat ive self-cleavage sites on both the positive and negative sense forms of the R N A , other regions of the sequence are quite dissimilar between the Canadian and Australasian strains.