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Classification and identification of geminiviruses using sequence comparisons

M Padidam1, R N Beachy, C M Fauquet

  • 1Division of Plant Biology-MRC7, Scripps Research Institute, La Jolla, CA 92037.

The Journal of General Virology
|February 1, 1995
PubMed
Summary
This summary is machine-generated.

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Geminiviruses can be classified into two main groups: leafhopper-transmitted monocot-infecting viruses and whitefly-transmitted dicot-infecting viruses. Coat protein sequences, particularly the N-terminal region, are useful for classifying geminivirus isolates.

Area of Science:

  • Virology
  • Bioinformatics
  • Plant Pathology

Background:

  • Geminiviruses are a significant group of plant viruses with diverse host ranges and transmission modes.
  • Accurate classification of geminiviruses is crucial for understanding their epidemiology and developing control strategies.

Purpose of the Study:

  • To classify geminiviruses based on genomic and open reading frame (ORF) sequence comparisons.
  • To investigate phylogenetic relationships and sequence identities within and between geminivirus subgroups.
  • To identify suitable genomic regions and sequences for robust geminivirus classification.

Main Methods:

  • Comparative analysis of genomes and ORFs from 36 geminivirus isolates.
  • Construction of phylogenetic trees and frequency distributions of pairwise sequence identities.

Related Experiment Videos

  • Analysis of intergenic regions and coat protein (CP) amino acid sequences.

    • Main Results:

    • Geminiviruses form two distinct clusters: subgroup I (leafhopper-transmitted, monocot-infecting) and subgroup III (whitefly-transmitted, dicot-infecting).
    • Sequence identity distributions within subgroups allow for taxonomic quantification; strains of the same virus share >90% identity.
    • The N-terminal region of the CP is highly variable and accurately represents the genome, suitable for isolate classification via PCR.

    Conclusions:

    • Genomic comparisons support a clear taxonomic structure for geminiviruses based on distinct subgroups.
    • The N-terminal CP sequence provides a reliable marker for classifying geminivirus isolates.
    • A proposed taxonomic framework integrates sequence data and biological characteristics for geminivirus classification.