1887

Abstract

Most of the genomic sequence of virus (CAV), previously called virus, has been determined. It is a ssRNA molecule of 9065 nt with at least four ORFs. At its 5′ 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 3′-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 5′ and 3′ 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.

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Supplements

vol. , part 11, pp. 2679–2690

GenBank accession numbers of sequences compared in Figs 2, 3, 5, 6 and 7.

The 12 longest ORFs in the virus sequence of 9065 nt.

Primers used for sequencing CAV RNA.

The pattern of nucleotide occurrence in all pairs of adjacent codons in ORFs 2, 7, 8 and 10.

Alignment of virus and benyvirus replicases.

The aligned amino acid sequences of the coat proteins of virus (JF824737); cucumber mottle tobamovirus (YP_908763); and tobacco mosaic tobamovirus (NC_001367), together with the predicted secondary structure of each residue of the sequences.



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