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Join us for a USDA-NIFA-sponsored workshop designed to introduce participants to a third- generation sequencing method for pathogen detection and identification. Participants will be encouraged to supply DNA from their fungal pathogen of interest to have hands-on practice in library preparation and sequencing using Nanopore MinIon sequencers. This method may be especially relevant to diagnosis of diseases caused by fastidious and unculturable pathogens. Additionally, we will focus on diseases of woody plants, as these remain some of the more recalcitrant tissues to process for downstream molecular work.
To increase sensitivity that will allow for 'in-planta' detection, participants will enrich diagnostic and phylogenetically informative loci using probes designed to target fungal pathogens. Analysis of sequence data for pathogen identification will finalize the course. Methods and open-source code will be made available on-line so that participants will have resources readily available and may contribute to the further development of diagnostic workflows post-workshop. Workshop materials and during-workshop meals are covered by the USDA-NIFA project; participants will need to fund their own travel and lodging.
Participants must have a working knowledge of and access to the infrastructure for basic nucleic acid amplification, gel purification, traditional sequencing, and BLAST analysis.





The UFIT Workshop is a USDA-NIFA funded event: USDA-NIFA-AFRI-Tactical Sciences for Agricultural Biosecurity-2021-68013-33758

Workshop Agenda (pdf)

DNA Extraction Protocol (doc)

2023 UFIT Workshop Protocol



DNA Submission Report


UFIT Workshop Presentations

Data Analysis Instructions