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Background  Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus  Hypocrea / Trichoderma .    Results  Here we report an analysis of the genome sequences of the two biocontrol species  Trichoderma atroviride  (teleomorph  Hypocrea atroviridis ) and  Trichoderma virens  (formerly  Gliocladium virens , teleomorph  Hypocrea virens ), and a comparison with  Trichoderma reesei  (teleomorph  Hypocrea jecorina ). These three  Trichoderma  species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to  T. reesei  or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that  T. reesei  and  T. virens  are derived relative to  T. atroviride . The mycoparasitism-specific genes thus arose in a common  Trichoderma  ancestor but were subsequently lost in  T. reesei .    Conclusions  The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma