The 5'-terminal sequences of the virion protein mRNAs of ononis yellow mosaic and kennedya yellow mosaic tymoviruses were determined, and also the positions in the genomes of the transcription initiation sites of those mRNAs. Comparisons of the available genomic sequences of tymoviruses revealed two conserved regions, one at the initiation site and another longer sequence of sixteen nucleotides to the 5' side of it. The longer sequence, which we call the tymobox, was tested as a target for a designed ribozyme, which cleaved appropriate genomic fragments of three tymoviruses. A synthetic oligonucleotide with sequence complementary to the tymobox was shown to be a tymovirus-specific probe for diagnosing and identifying tymoviruses, except for wild cucumber mosaic tymovirus. The tymobox sequence was also used as a primer for the second strand DNA synthesis of dsDNA representing the virion protein gene of cacao yellow mosaic tymovirus, a tymovirus with unknown sequence. Thus, the tymobox is a useful tool in molecular studies of tymoviruses.

Most of the genomic sequence of Chara australis virus (CAV), previously called Chara corallina virus, has been determined. It is a ssRNA molecule of 9065 nt with at least four ORFs. At its 59 end is an ORF encoding a protein of 227 kDa, distantly homologous to the multifunctional replicases of benyviruses and rubiviruses. Next is an ORF encoding a protein of 44 kDa, homologous to the helicases of pestiviruses. The third ORF encodes an unmatched protein of 38 kDa that is probably a movement protein. The fourth and 39-terminal ORF encodes a protein of 17.7 kDa homologous to the coat proteins of tobamoviruses. The short methyltransferase region of the CAV replicase matches only the C-terminal motif of benyvirus methyltransferases. This and other clues indicate that approximately 11 % and 2 % of the 59 and 39 termini of the complete CAV genome, respectively, are missing from the sequence. The aligned amino acid sequences of the CAV proteins and their nearest homologues contain many gaps but relationships inferred from them were little affected by removal of these gaps. Sequence comparisons show that three of the CAV genes may have diverged from the most closely related genes of other viruses 250-450 million years ago, and the sister relationship between the genes of CAV and those of benyviruses and tobamoviruses, mirroring the ancient sister relationship between charophytes (i.e. the algal host of CAV) and embryophytes (i.e. the plant hosts of tobamoviruses and benyviruses), is congruent with this possibility. INTRODUCTIONA large charophyte alga growing in the Murrumbidgee River near Canberra, Australia was reported to be infected with a tobamovirus (Gibbs et al., 1975;Skotnicki et al., 1976). The host was identified as Chara corallina var. corallina K. ex Willd., but more recently this species has been reclassified and named Chara australis var. nobilis (A. Braun) R. D. Wood (http://data.gbif.org/search/chara%20australis; http://www. algaebase.org/search/species/detail/?species_id=27145). This species is rightly called 'nobilis' as individual plants are up to 2 m in length, and their coenocytic internodal cells are up to 100 mm in length! The virus was reported to be a tobamovirus as its virions closely resembled those of tobacco mosaic tobamovirus (Zaitlin, 2000) except that their modal length was approximately 530 nm, rather than the 300 nm of all reported tobamoviruses. Moreover, preparations of its virions reacted with high-titre antisera prepared against the virions of tobacco mosaic and odontoglossum ringspot viruses, but not those of several other tobamoviruses. The new virus was named Chara corallina virus, but with the updated nomenclature of the host, we now call it Chara australis virus (CAV).Up to 22 % of the naturally infected Chara plants first found contained CAV virions, and some infected cells contained birefringent inclusions, like those found in tobacco mosaic virus (TMV)-infected plants (Sheffield, 1934;Steere & Williams, 1953). Healthy C. australis plants became infected when injected with viri...

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EMBL accession no. X54354Cacao yellow mosaic virus (CoYMV), isolated from leaves of West African Amelonado cacao, was shown to be a member of