A type of nucleotide motif that distinguishes tobamovirus species more efficiently than nucleotide signatures

A. J. Gibbs*, J. S. Armstrong, M. J. Gibbs

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    32 Citations (Scopus)

    Abstract

    The complete genomic sequences of forty-eight tobamoviruses were classified and found to form at least twelve species clusters. Individual species were not conveniently defined by 'nucleotide signatures' (i.e. strings of one or more nucleotides unique to a taxon) as these were scattered sparsely throughout the genomes and were mostly single nucleotides. By contrast all the species were concisely and uniquely distinguished by short nucleotide motifs consisting of conserved genus-specific sites intercalated with variable sites that provided species-specific combinations of nucleotides (nucleotide combination motifs; NC-motifs). We describe the procedure for finding NC-motifs in a convenient and phylogenetically conserved region of the tobamovirus RNA polymerase gene, the '4404-50 motif'. NC-motifs have been found in other sets of homologous sequences, and are convenient for use in published taxonomic descriptions.

    Original languageEnglish
    Pages (from-to)1941-1954
    Number of pages14
    JournalArchives of Virology
    Volume149
    Issue number10
    DOIs
    Publication statusPublished - Oct 2004

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