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United States Department of Agriculture

Agricultural Research Service

Research Project: EXOTIC, EMERGING, RE-EMERGING, AND INVASIVE PLANT DISEASES OF HORTICULTURAL CROPS

Location: Horticultural Crops Research

Title: The Promise and Pitfalls of Sequence-Based Identification of Plant Pathogenic Fungi and Oomycetes.

Authors
item Kang, S -
item Mansfield, M -
item Park, B -
item Geiser, D -
item Ivors, K -
item Coffey, M -
item GRUNWALD, NIKLAUS
item MARTIN, FRANK
item Levesque, C -
item Blair, J -

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 10, 2010
Publication Date: August 2, 2010
Citation: Kang, S., Mansfield, M., Park, B., Geiser, D., Coffey, M., Grunwald, N.J. 2010. The promise and pitfalls of sequence-based identification of plant pathogenic fungi and oomycetes. Phytopathology. 100: 732-737.

Interpretive Summary: Identification of plant pathogens remains a challenging task. Traditionally fungal microorganisms were identified using microscopic techniques. Contemporary analysis typically relies on analysis of selected genetic DNA sequences. Although DNA based approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own shortcomings. Here, we outline the potential benefits and drawbacks of using publicly accessible sequence databases for identification of plant pathogenic fungi and fungus-like organisms,using Phytophthora as a primary example. We also discuss potential improvements for these pitfalls and the question of why coordinated community efforts are essential to making such remedies more efficient and robust.

Technical 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 shortcomings. Here, we outline the potential benefits and drawbacks of using publicly accessible sequence databases for identification and taxonomic deductions of plant pathogenic fungi and fungus-like organisms,using Phytophthora as a primary example; we also discuss potential remedies for these pitfalls and the question of why coordinated community efforts are essential to making such remedies more efficient and robust.

Last Modified: 9/10/2014
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