Molecular criteria for genus and species discrimination within the family Potyviridae View Full Text


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Article Info

DATE

2005-03

AUTHORS

M. J. Adams, J. F. Antoniw, C. M. Fauquet

ABSTRACT

A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance. More... »

PAGES

459-479

References to SciGraph publications

  • 1997-11. Phylogenetic analysis of the Potyviridae with emphasis on legume-infecting potyviruses in ARCHIVES OF VIROLOGY
  • 2001-12. Molecular evidence that the aphid-transmitted Tomato mild mottle virus belongs to the Potyviridae family but not the Potyvirus genus in ARCHIVES OF VIROLOGY
  • 2004-08. The nucleotide sequence of Watermelon mosaic virus (WMV, Potyvirus) reveals interspecific recombination between two related potyviruses in the 5′ part of the genome in ARCHIVES OF VIROLOGY
  • 1992. Potyviruses, chaos or order? in POTYVIRUS TAXONOMY
  • 2003-01. Virology division news: Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species in ARCHIVES OF VIROLOGY
  • 2002-09. Taxonomic position of sugarcane streak mosaic virus in the family Potyviridae* in ARCHIVES OF VIROLOGY
  • 1970-01. The identification of three new viruses isolated from Wisteria and Pisum in The Netherlands, and the problem of variation within the potato virus Y group in NETHERLANDS JOURNAL OF PLANT PATHOLOGY
  • 1992. Designation of potyvirus genera: a question of perspective and timing in POTYVIRUS TAXONOMY
  • 2004-08. The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation in ARCHIVES OF VIROLOGY
  • 1992. Present status of the sugarcane mosaic subgroup of potyviruses in POTYVIRUS TAXONOMY
  • 2002-06. Bean common mosaic virus isolates causing different symptoms in asparagus bean in China differ greatly in the 5′-parts of their genomes in ARCHIVES OF VIROLOGY
  • 1989-03. Coat protein of Potyviruses in ARCHIVES OF VIROLOGY
  • 2004-02. A virus related to Soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates in ARCHIVES OF VIROLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00705-004-0440-6

    DOI

    http://dx.doi.org/10.1007/s00705-004-0440-6

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1041246410

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/15592889


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