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

Phytopathology
Seogchan KangJaime E Blair

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 interpretation 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 deduction 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.

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Citations

Jan 16, 2014·Indian Journal of Virology : an Official Organ of Indian Virological Society·K PrabhaR K Jain
Mar 17, 2011·Phytopathology·Melanie N MitchellDavid H Gent
May 23, 2012·Annual Review of Phytopathology·Solke H De Boer, María M López
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Oct 7, 2011·Molecular Ecology Resources·Ashwin NaiduMelanie Culver
Mar 10, 2016·Studies in Mycology·D A HerronE T Steenkamp
Aug 22, 2013·Phytopathology·Bongsoo ParkSeogchan Kang
Dec 16, 2017·IMA Fungus·Xiao YangChuanxue Hong
May 1, 2013·Plant Disease·A J LeonbergerJ L Beckerman
Jun 1, 2012·Plant Disease·Jean Beagle Ristaino
Jan 1, 2015·Plant Disease·Kimberly K Zitnick-Anderson, Berlin D Nelson
Mar 1, 2011·Plant Disease·Niklaus J GrünwaldJennifer L Parke

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