Nanopore high-throughput sequencing for resolution of problems in plant pathogen epidemiology and diagnostics




Project acronym: NanoPhyto
Funding from: Croatian Science Foundation
Duration: October 01, 2020 – September 30, 2023, extended until January 15, 2024
Principal investigator: Prof. dr. sc. Dijana Škorić
Budget: 1.310.252,50 hrk
Project number and type: IPS-2020-01-2960 (Research Projects – Slovenian-Croatian bilateral projects)

The aim of the project NanoPhyto is to make use of the tomato cultivation systems as a case study to demonstrate and improve the usefulness of Nanopore high throughput sequencing (HTS) technology in deciphering complex aetiologies of plant diseases. The plant pathogen complexes may involve one or more viruses of different genome types (e.g. dsDNA, ssRNA, dsRNA), viroids (small circular RNA plant pathogens), possibly phytoplasmas, and their combinations. The wild plants out of the tomato cultivation area borders will be included in the analyses as potential pathogen reservoirs. In addition, the irrigation waterways will be tested as possible, but under investigated, pathogen transmission routes. This approach should provide insight into the molecular epidemiology of the tomato diseases and ecology of the selected (agro)ecosystems. The obtained metagenomic screenshot of the surveyed tomato (agro)ecosystems will help developing plant virology and microbial ecology research in Croatia. The project will provide the testing system for the improvement of Nanopore HTS application in plant pathology and environmental microbiology pioneered by the Slovenian team. Besides building research expertise in Croatia, it will introduce novel HTS technologies in plant molecular microbiology and provide new data on the occurrence and diversity of tomato viruses and other virus-like pathogens. This glimpse into tomato diseases may result in novel ideas for the development of the disease management strategies based on the molecular epidemiology and ecology knowledge.