The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes.
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.
Kang
Seogchan
S
Mansfield
Michele A
MA
Park
Bongsoo
B
Geiser
David M
DM
Ivors
Kelly L
KL
Coffey
Michael D
MD
Grünwald
Niklaus J
NJ
Martin
Frank N
FN
Lévesque
C André
CA
Blair
Jaime E
JE
D048028:DNA, Algal; D004271:DNA, Fungal; D030561:Databases, Nucleic Acid; D005658:Fungi / Q000145:classification* / Q000235:genetics; D010838:Phytophthora / Q000145:classification* / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology*; D017422:Sequence Analysis, DNA
D048028:DNA, Algal; D004271:DNA, Fungal