Exploring the Genetic and Molecular Mechanisms Underlying the Interaction Between Tomato and Endophytic Fungi: A Bioinformatic Analysis and Review of Key Genes and Pathways

Endophytic fungi are known to improve plant resistance to stress and enhance plant performance. A comprehensive understanding of the mechanisms underlying endophytic fungi-mediated systemic resistance is crucial for the widespread adoption of these fungi as beneficial biological control agents. To unravel the complex interactions between tomato and endophytic fungi, we compared the transcriptomic responses of tomato plants induced with Trichoderma harzianum, T. afroharzianum, T. atroviride and Pochonia chlamydosporia. RNA-seq datasets were used to assess the common expression patterns in defence-related pathways. Our analysis revealed that a group of common key genes were significantly induced in all investigations examined. Additionally, we observed that 20 transcripts related to anion transport, which is crucial for early plant immune responses, were consistently enriched in all the studies. These findings highlight the conserved and specific nature of plant–endophyte interactions and their potential for enhancing plant resistance through targeted genetic manipulation and breeding for long-lasting resistance.