The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes

Seogchan Kang, Michele A. Mansfield, Bongsoo Park, David M. Geiser, Kelly L. Ivors, Michael D. Coffey, Niklaus J. Grunwald, Frank N. Martin, C. André Lévesque, Jaime E. Blair

Research output: Contribution to journalReview article

Abstract

Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence- based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified inter-pretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deductions of plant-pathogenic fungi and oomycetes, using Phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.

Original languageEnglish (US)
Pages (from-to)732-737
Number of pages6
JournalPhytopathology
Volume100
Issue number8
DOIs
StatePublished - Aug 1 2010
Externally publishedYes

Keywords

  • Culture collection
  • DNA barcode
  • Database
  • Diagnosis
  • Phylogeny
  • Taxonomy

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science

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  • Cite this

    Kang, S., Mansfield, M. A., Park, B., Geiser, D. M., Ivors, K. L., Coffey, M. D., Grunwald, N. J., Martin, F. N., Lévesque, C. A., & Blair, J. E. (2010). The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes. Phytopathology, 100(8), 732-737. https://doi.org/10.1094/PHYTO-100-8-0732