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Research Project: Identification, Characterization, and Biology of Foreign and Emerging Viral and Bacterial Plant Pathogens

Location: Foreign Disease-Weed Science Research

Title: Screening metagenomic data for viruses using the E-Probe Diagnostic Nucleic Acid Assay (EDNA)

item STOBBE, ANTHONY - Pennsylvania State University
item Schneider, William
item HOYT, PETER - Oklahoma State University
item MELCHER, ULRICH - Oklahoma State University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2014
Publication Date: 10/1/2014
Citation: Stobbe, A.H., Schneider, W.L., Hoyt, P., Melcher, U. 2014. Screening metagenomic data for viruses using the E-Probe Diagnostic Nucleic Acid Assay (EDNA). Phytopathology. 104:1125-1129.

Interpretive Summary: One of the most critical weapons in the fight against plant diseases is early detection, the ability to correctly identify the microbe that is causing a given disease outbreak. Many plant disease detection assays exist, but the vast majority of these assays are limited to identifying a single microbe at a time. A new technology, called next-generation sequencing, was developed for determining the genetic sequence of organisms. This technology has been used as a tool to detect microbes, but the huge amount of data generated by the technology makes next-generation sequencing microbe detection difficult and unwieldy. To correct this problem, a new computer software tool was developed, called E-probe Diagnostic Nucleic acid Assay (EDNA). This tool has the ability to ignore a lot of the less useful information that is generated by next-generation sequencing technologies, seeking out microbial sequences of interest in a manner similar to a Google search of web pages. EDNA was successfully used to detect two very different plant viruses from infected plants analyzed by next-generation sequencing. In addition, EDNA run on a simple laptop was 2400 time faster than the traditional sequence analysis computer programs run on a supercomputer. This technology represents a significant step forward in turning a highly powerful sequencing technology into a very useful plant disease detection technology.

Technical Abstract: There are many plant pathogen-specific diagnostic assays, based on PCR and immune-detection. However, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitations during assembly and similarity searching of sequence data which extend the time needed to make a diagnostic decision. The E-probe Diagnostic Nucleic acid Assay (EDNA) process provides the framework for a new sequence-based detection system which eliminates the need for assembly of NGS data. EDNA was applied to two plant viruses, Plum pox virus (PPV) and Bean golden mosaic virus (BGMV) as a proof of concept. PPV is an RNA virus, and BGMV is a DNA virus. EDNA was successful in detecting both viruses from an infected plant sample metagenome. Perhaps most significantly, EDNA run on a simple laptop was 2400 times faster than traditional metagenome analyses that were run on a supercomputer. This study shows that EDNA is a successful tool for dealing with large volumes of complex metagenome data in a consistent and versatile manner.