Comparative sequence and structure of different isolates of citrus exocortis viroid

Abstract

The nucleotide sequences of two new Australian isolates of citrus exocortis viroid (CEV), CEV-DE25 and CEV-DE26, have been determined and compared with the previously sequenced Australian isolate, CEV-A (J. E. Visvader, A. R. Gould, G. E. Breuning, and R. H. Symons. FEBS Lett. 137, 288–292 (1982).) and a Californian isolate, CEV-C (H. J. Gross, G. Krupp, H. Domdey, M. Raba, P. Jank, C. Lossow, H. Alberty, K. Ramm, and H. L. Sanger. Eur. J. Biochem. 121, 249–257 (1982).). Sequencing of recombinant DNA clones prepared from purified CEV-A showed sequence heterogeneity at four nucleotide residues which was not observed by direct RNA sequencing. The data indicated that purified CEV-A contained minor amounts of at least one other CEV species designated CEV-AM. All isolates contain 371 residues. In comparison with the sequence of CEV-A, four residues are different in CEV-C and CEV-DE25 while CEV-DE26 has 27 nucleotide differences which include exchanges, insertions, and deletions. Most of the nucleotide differences in CEV-C, CEV-DE25, and CEV-DE26 alter the proposed secondary structure relative to CEV-A. No nucleotide differences were found to occur in the highly conserved central region previously shown to be present in the predicted native structures of CEV, potato spindle tuber viroid, chrysanthemum stunt viroid, and coconut cadang-cadang viroid.