High-Throughput Sequencing in Phytopathology: Genomics-Driven Diagnostics and Host-Pathogen Interactions

Plant diseases severely constrain agricultural productivity, exacerbating food insecurity, economic instability, and environmental degradation. Global trade and climate change further intensify pathogen spread, emergence, and host shifts. While traditional diagnostics and targeted assays, such as PCR and ELISA, improve specificity, they depend on prior knowledge and are limited in detecting novel or mixed infections. High-throughput sequencing (HTS) has emerged as a transformative, unbiased platform that allows comprehensive detection of known and unknown pathogens through metagenomics and transcriptomics. By generating large-scale genomic data, HTS supports pathogen discovery, epidemiological surveillance, quarantine systems, and genome-informed disease management. It underpins advanced strategies, including CRISPR-Cas editing and RNA interference, and accelerates the breeding of resistance. Despite challenges—such as bioinformatics standardization, cost, and data interpretation—HTS, when integrated with classical diagnostics and biological validation, represents a foundational technology for sustainable, proactive plant health management and global phytosanitary resilience.