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A systematic approach for developing molecular markers for Oomycetes

Frank Martin: USDA ARS

<div>Having a systematic approach for designing amplification primers for genes that are useful for isolate identification & phylogenetic studies, population studies, diagnostic assays, and metagenomic studies would enhance research opportunities. This is particularly true for Oomycetes due to the difficulty in morphology-based species classification and the obligate nature of some taxa. To address this need, the mitochondrial genomes of over 500 isolates representing 155 taxa for a range of Oomycetes have been assembled and comparative genomics conducted. Gene order differences compared to plant and Eumycotan fungal genomes have been useful for development of specific primers for amplification of genes (<em>rps10</em>) from a wide range of taxa (including downy mildews) and design of diagnostic assays. A single assay capable of detecting <em>Phytophthora </em>at a genus and species-specific level has been validated with data supporting development of species-specific TaqMan probes for 89% of the genus. Similar types of assays are in development for <em>Pythium, Aphanomyces</em> and several downy mildews. Unique putative open reading frames also are useful for design of species-specific diagnostic assays for pathogen detection and quantification (<em>Bremia lactucae</em>). Mitochondrial genome assembly for multiple isolates of the same species has identified loci useful for haplotype classification in population studies, and some of the loci noted above are also useful in metagenomics studies.</div>