Plant-pathogen interactions: making the case for multi-omics analysis of complex pathosystems

Understanding plant-pathogen interactions requires a systems-level perspective that single-omics approaches, such as genomics, transcriptomics, proteomics, or metabolomics alone, often fail to provide. While these methods are informative, they are limited in their ability to capture the complexity of the dynamic molecular interactions between host and pathogen. Multi-omics strategies offer a powerful solution by integrating complementary data types, enabling a more comprehensive view of the molecular networks and pathways involved in disease progression and defence. Although technological advances have made omics analyses more accessible and affordable, their integration remains underutilised in plant science. This review highlights the limitations of single-omics studies in dissecting plant-pathogen interactions and emphasises the value of multi-omics approaches. We discuss available computational tools for data integration and visualisation, outline current challenges, including data heterogeneity, normalisation issues, and computational demands, and explore future directions such as the exploitation of artificial intelligence-based approaches and single-cell omics. We conclude that the increasing accessibility and affordability of omics analysis means that multi-omics strategies are now indispensable tools to investigate complex biological processes such as plant-pathogen interactions.