EDNA-Wheat, A Massive Parallel Sequencing Based Tool for Detection of Wheat Viruses
Astri Wayadande: Oklahoma State University
<div>Each year, wheat growers lose significant yields to arthropod transmitted viruses and accurate diagnosis is essential for management. Electronic probe diagnostic nucleic acid analysis (EDNA) is a next generation sequencing (NGS) based diagnostic tool where highly curated, target-specific electronic probes (e-probes), 30-120 nucleotides in length, are used to query unassembled metagenomic databases for detecting the presence of target nucleic acid sequences. E-probes, 30 nucleotides in length and specific to 17 wheat infecting viruses, including three strains of <em>Barley yellow dwarf virus </em>(BYDV-MAV, -PAV and -PAS) were designed, curated and validated in mock metagenomic databases generated using MetaSim and metatranscriptomic data obtained from healthy wheat tissue. To predict the sensitivity of EDNA as a diagnostic tool for the detection of viruses in wheat metagenomic data, two viruses, <em>Wheat streak mosaic virus</em> (WSMV) and BYDV, were selected as models to assess detection limits. Detection of all 17 viral pathogens of wheat and discrimination between three strains of BYDV was demonstrated in both single and multiple mock, <em>in-silico</em> infections. Thirty-five mock¸ <em>in-silico</em> metagenomic databases were generated with a known number of virus reads for WSMV and three strains of BYDV. It was determined that EDNA could detect a minimum of 31 virus reads out of a total of 10 million reads (0.00031%) (p=0.04332).</div>
View Presentation |
