Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.
Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.
Agriculture & Agri-Food Canada, Central Experimental Farm, Ottawa, Ontario K1A 0C6, Canada.
Wen
W
Chen
Zeinab Robleh
ZR
Djama
Michael D
MD
Coffey
Frank N
FN
Martin
Guillaume J
GJ
Bilodeau
Lorien
L
Radmer
Geoff
G
Denton
C André
CA
Lévesque
D016000:Cluster Analysis; D003575:Cytochromes c1 / Q000235:genetics; D045362:Cytochromes c2 / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005240:Feasibility Studies; D005819:Genetic Markers / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D010802:Phylogeny; D010838:Phytophthora / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D010935:Plant Diseases / Q000469:parasitology*; D018515:Plant Leaves / Q000469:parasitology; D018517:Plant Roots / Q000469:parasitology; D018547:Plant Stems / Q000469:parasitology; D010944:Plants / Q000469:parasitology*; D016133:Polymerase Chain Reaction; D011775:Pythium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D012987:Soil; D013045:Species Specificity
D021901:DNA, Intergenic; D021903:DNA, Ribosomal Spacer; D005819:Genetic Markers; D009841:Oligonucleotides; D012987:Soil; D003575:Cytochromes c1; D045362:Cytochromes c2