Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

Chen, W., Robleh Djama, Z., Coffey, M.D., Martin, F.N., Bilodeau, G.J., Radmer, L., Denton, G., and Lévesque, C.A. (2013). "Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.", Phytopathology, 103(1), pp. 43-54. doi : 10.1094/PHYTO-04-12-0092-R  Access to full text

Abstract

Most Phytophthora species are destructive plant pathogens so 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 species 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, CS). Each sequence dataset contained approximately 250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, non-rejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora species, including several quarantine or regulated pathogens such as P. 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 species from complex environmental samples without the need for extensive growth of cultures.

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