Agriculture, the cornerstone of food production, faces a relentless challenge from microbial pathogens that threaten crop yields, food security, and environmental sustainability. Effective identification and characterization of these agricultural pathogens are essential for implementing targeted disease management strategies. (Villamor et.al. 2019; Prajapati et al. 2023) High throughput sequencing (HTS) has emerged as a powerful tool to unravel the complexity of microbial communities within agricultural ecosystems, aiding in the identification, characterization, and monitoring of pathogens. HTS, including next-generation sequencing (NGS) and third-generation platforms, has revolutionized agricultural microbiology. It enables comprehensive assessments of genetic diversity and microbial population dynamics affecting crops, soil, and the agroecosystem. This knowledge empowers researchers to identify known pathogenic species, discover novel threats, and gain insights into virulence mechanisms, host interactions, and environmental factors influencing pathogen dynamics. Applications of HTS in agricultural pathogen identification span viruses, bacteria, fungi, nematodes, and other biotic stressors. Addressing challenges in HTS data analysis, such as data management, quality control, and multi-omics dataset integration, is crucial for informed decision-making for farmers and agronomists. Furthermore, HTS supports sustainable agriculture by enabling precision disease management, reducing pesticide usage, and facilitating disease-resistant crop development. It offers the potential for rapid detection and early warning systems in agricultural settings.

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