Mitochondrial Genomics: A systematic method for development of loci for diagnostics, taxonomy, phylogenetics and metagenomic studies

Authors: Martin, Frank

Submitted to: International Congress of Plant Pathology Abstracts and Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 3/26/2018
Publication Date: 7/28/2018
Citation: Martin, F.N. 2018. Mitochondrial Genomics: A systematic method for development of loci for diagnostics, taxonomy, phylogenetics and metagenomic studies. International Congress of Plant Pathology, 6th International Oomycetes Workshop: Phytophthora, Pythium, Downy Mildews and Related Genera, July 28, 2018, Boston, Massachusetts.

Interpretive Summary: Oomycetes are a group of fungal like organisms that are important plant pathogens and can be difficult to identify due to overlapping morphological features. In an effort to develop a systematic approach for designing amplification primers that can be used on a wide range of taxa as well as diagnostic assays for pathogen detection, the mitochondrial genomes for a wide range of taxa have been assembled. Comparative genomics is providing insight to how the genomes evolve and a dataset useful for the systematic development of primers and probes. The results of this work provides a resource for other researchers and regulatory personnel.

Technical Abstract: Having a systematic approach for designing amplification primers for loci that are useful for taxonomic, phylogenetic, population, and metagenomic studies, as well as diagnostic assays, would enhance Oomycete research opportunities. To address this opportunity, the mitochondrial genomes of over 550 isolates representing 155 taxa for a range of Oomycetes were assembled and comparative genomics conducted. Gene order differences relative to plant and Eumycotan fungi are useful for development of specific primers for amplification of loci from a wide range of taxa (including downy mildews) and design of diagnostic assays. A single assay capable of detecting Phytophthora at a genus and species-specific level was developed with taxon specific markers validated for 50 species and the sequence data indicating species-specific TaqMan probes could be developed for 89% of the genus. Similar types of assays are in development for Pythium, Aphanomyces and several downy mildews. Unique putative open reading frames also are useful for design of species-specific diagnostic assays for detection and quantification. Polymorphic regions of the genome have also been useful for identification of loci to characterize mitochondrial haplotypes for population studies.