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

First to fourth authors: Department of Plant Pathology, The Pennsylvania State University, University Park 16802; fifth author: Mountain Hort. Crops Research & Extension Center, North Carolina State University, Mills River 28759; sixth author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; seventh author: Horticultural Crops Research Laboratory, USDA-ARS and Department of Botany & Plant Pathology, Oregon State University, Corvallis 97330; eighth author: USDA-ARS, Salinas, CA 93906; ninth author: Agriculture and Agri-Food Canada, Ottawa K1A 0C6, Canada; and tenth author: Department of Biology, Franklin & Marshall College, Lancaster, PA 17604.

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 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.

Additional keywords: culture collection, database, diagnosis, DNA barcode, phylogeny, taxonomy.