A Comprehensive Genome-Based Diagnostics Resource and Pipeline for Identification of Threatening Plant Pathogens

NON-TECHNICAL SUMMARY: There is a need for a comprehensive resource for plant pathogen genomic data for diagnosticians to obtain genomic sequence and annotation data to develop diagnostic markers for plant pathogens. We will develop a comprehensive, centralized resource for plant pathologists to obtain genomic (genome sequence) data for plant pathogens. We will obtain, store, and display, all publicly available sequence information for viral, bacterial, oomycete, fungal, and nematode plant pathogens. For all of these pathogen genomes, we will annotate the genomes for gene function. In addition, we will perform a series of computations on the data to identify conserved and diverged sequences within these genomes to identify putative markers (unique sequences) that can be used in diagnostics of these pathogens. We will demonstrate the use of a genomics approach in diagnostics of plant pathogens by developing diagnostic markers for three significant plant pathogens: Pythium, Xanthomonas, and Meloidogyne. To ensure this resource is utilized, we will provide training in genomics and our database to diagnosticians. This centralized resource will greatly facilitate researchers in developing diagnostic tools for plant pathogens.

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APPROACH: We will utilize a genomics approach to improve our diagnostic abilities in plant biosecurity. We will construct a comprehensive database for plant pathogen genomic sequence and annotation data. We will use computational tools to predict potential diagnostic markers in all pathogens with genomic data in the database. We will develop diagnostic markers for three pathogens of importance to US agriculture for a proof-of-concept of our approach. We will provide training to diagnosticians in the form of workshops in which participants are trained in genomic methodologies.