P-623 - Improving Field-Based Diagnosis of Phytophthora capsici with Optimized Nanopore Sequencing

Abstract Text: Phytophthora capsici (P. capsici) is a major pathogen that affects the production of cucurbitaceous crops. To identify these pathogens visually is challenging, often causing misdiagnoses, post-harvest rot, and confusion with symptoms from other pathogens or co-infections. Without timely, accurate diagnosis, P. capsici spreads rapidly, leading to significant crop losses. Established diagnostics like microscopy-based culture and polymerase chain reaction (PCR) are often slow and lack sensitivity for early-stage infections. This research introduces an optimized Oxford Nanopore Technology (ONT) genomic method for swift, precise P. capsici detection in plant material, suitable for both laboratory and field settings. Plant tissue samples (symptomatic and non-symptomatic) were collected by collaborators from cucurbit and pepper fields in late summer/early fall in 2024. Total DNA was extracted using a magnetic bead-based kit (Primerdesign, UK). Sequencing libraries were prepared with ONT’s 1D-cDNA sequencing kit, loaded onto a MinION 107 v9.5 Flow Cell, and analyzed using the Mk1B MinION device. Raw fast5 sequence reads were converted to fastq/fasta; high-quality reads were then subjected to BLAST searches against the NCBI database for P. capsici identification. The deployment of ONT allows for real-time generation of actionable genomic data, enhancing understanding of P. capsici infection in cucurbits. This technology represents a significant advancement in rapid, field-based diagnosis of P. capsici, providing farmers with an efficient tool to mitigate crop losses.