Trichoderma in multitrophic plant-microbe interactions: a pan-genome guided roadmap for resilient physiology and sustainable bio-economy

By 2050, the global population is projected to reach 9 billion, necessitating innovative approaches beyond traditional agricultural methods to ensure adequate food security. Several biological control agents have been used throughout the world to control plant diseases by re-programming natural prey-predator interactions. Trichoderma's biocontrol capabilities and plant growth-promoting effects have been extensively studied and documented, paving the way for its widespread adoption in agricultural practices. Here we performed a comprehensive pan-genome analysis of 25 industrially and agriculturally important Trichoderma strains, revealing an open pan-genome indicative of continuous genetic innovation. A combined total of 4960 core genes were shared between both industrial and biocontrol strains, which encode for fundamental functions with accessory and unique genes being enriched in adaptive functions. Industrial strains like T. reesei QM6a with 322 unique genes had enrichment of features for secretion of cellulase and lignocellulose degradation, validating their commercial dominance in industries producing enzymes and biofuels, while biocontrol-associated strains like T. harzianum CBS226.95 and T. virens Gv29-8 showed expanded accessory gene repertoires enriched in defense-related functions and secondary metabolism. Comparative biosynthetic gene cluster analysis across 25 genomes further demonstrated pronounced strain-level variation. Core-genome phylogeny revealed conserved ancestral relationships, whereas pan-genome phylogeny highlighted accessory gene-driven divergence among closely related strains. Remarkably, many strains had dual promise, being both industrial producers of enzymes and agriculturally desirable, highlighting their interdisciplinary applications. These results demonstrate the genomic malleability of Trichoderma and the adaptability of its evolution, facilitating agriculture and biotechnology, and provide a template for strain selection with precision and rational bioformulation design for promoting sustainable agriculture, environmental robustness, and green industry.