EDNA-host: Detection of global plant viromes using high throughput sequencing

Abstract

The aim of this research was to develop the concept of host-specific virome detection methods. Three model systems were selected roses, cucurbits, and water. EDNA MiFi was used to generate pathogen electronic probes (E-probes) for the detection of viruses in-silico and in-vitro using field samples for validation. The selected three host model allows a comprehensive detection system for specifically targeting the three pre-determined host viromes (117 plant viruses). This research also presents a validation of the analytical sensitivity determining the in-vitro limit of detection (10pg) quantified for a specific set of E-probes (ArMV-RNA2 60nt). The database of EDNA-Rose MiFi includes E-probes (523) specifically designed to detect 22 reported viruses infecting roses worldwide. The EDNA-Cucurbits MiFi includes E-probes (412) for 15 reported viruses. Finally, the MiFi database EDNA-Water is composed of a selection of highly specific E-probes (1730) for 80 reported viruses within the genera Potexvirus, Tobamovirus, and Tombusvirus. The detection of the presence of multiple viruses in a host is challenging. Hence, the relevance of developing and applying a broad detection system to detect viruses out of a virome in a sample. The application of EDNA-Host extends to plant virus detection to all staple crops, virus-free certification programs, breeding, veterinary and life sciences.