Genomic and epigenomic insights into Trichoderma–plant interactions

Abstract

Trichoderma is a globally distributed beneficial fungus found in soils, plant residues, and roots, and has been widely used in agriculture to promote seed germination and enhance seedling growth, resistance, and fruit yield. It supports plant growth through diverse mechanisms, including direct antagonism of pathogens, induction of plant resistance, modulation of beneficial microbial communities, improvement in nutrient uptake, and stimulation of phytohormone synthesis. Recent advances in genomic and epigenomic research have provided deeper insights into the molecular mechanisms underlying the mutualistic interactions between Trichoderma and plants. This review summarizes these advances from genomic and epigenetic perspectives, highlighting the roles of secondary metabolite gene clusters, transposable elements, chromatin-level regulation, and epigenetic priming in plant-beneficial traits. We also discuss emerging strategies that leverage genomic and epigenomic tools to study and enhance Trichoderma’s biocontrol potential, aiming to optimize its application in sustainable agriculture.