Plant disease caused by fungus is one of the major threats to global food security, and understanding fungus–plant interactions is important for plant disease control. Research devoted to revealing the mechanisms of fungal pathogen–plant interactions has been conducted using genomics, transcriptomics, proteomics, and metabolomics. Metabolomics research based on mass spectrometric techniques is an important part of systems biology. In the past decade, the emerging field of metabolomics in plant pathogenic fungi has received wide attention. It not only provides a qualitative and quantitative approach for determining the pathogenesis of pathogenic fungi but also helps to elucidate the defense mechanisms of their host plants. This review focuses on the methods and progress of metabolomics research in fungal pathogen–plant interactions. In addition, the prospects and challenges of metabolomics research in plant pathogenic fungi and their hosts are addressed.
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