A high-throughput sequencing approach was utilized to carry out a comparative transcriptome analysis of Trichoderma atroviride IMI206040 during mycoparasitic interactions with the plant-pathogenic fungus Rhizoctonia solani. In this study, transcript fragments of 7,797 Trichoderma genes were sequenced, 175 of which were host responsive. According to the functional annotation of these genes by KOG (eukaryotic orthologous groups), the most abundant group during direct contact was "metabolism." Quantitative reverse transcription (RT)-PCR confirmed the differential transcription of 13 genes (including swo1, encoding an expansin-like protein; axe1, coding for an acetyl xylan esterase; and homologs of genes encoding the aspartyl protease papA and a trypsin-like protease, pra1) in the presence of R. solani. An additional relative gene expression analysis of these genes, conducted at different stages of mycoparasitism against Botrytis cinerea and Phytophthora capsici, revealed a synergistic transcription of various genes involved in cell wall degradation. The similarities in expression patterns and the occurrence of regulatory binding sites in the corresponding promoter regions suggest a possible analog regulation of these genes during the mycoparasitism of T. atroviride. Furthermore, a chitin-and distance-dependent induction of pra1 was demonstrated.Due to hazardous chemical fungicides affecting human health (4) and the environment (9), the application of biological control agents like Trichoderma spp. is a promising alternative for plant protection (17). Members of the genus Trichoderma (teleomorph Hypocrea) are potent mycoparasitic fungi that not only compete for nutrients but also secrete cell wall-degrading enzymes (CWDEs) such as chitinases, glucanases, and proteases, among others, and excrete secondary metabolites that are active against a number of plant-pathogenic fungi (15,28,29,41,58). In addition to an increase in enzyme secretion during interactions with host fungi, it was shown previously that differentiation processes occur, leading to morphological changes and the formation of penetration structures in mycoparasitic Trichoderma spp. (7,22). Interestingly, mycoparasitism is not a mere result of physical contact but may be proceeded by an early recognition process that leads to the induction of gene expression of hydrolytic enzymes (e.g., prb1 [18] and ech42 [67]).In recent years, a number of studies have identified enzymes and effectors involved in host recognition and the mycoparasitic responses of Trichoderma (40, 46, 51); however, their modes of action and the mechanisms determining host specificity remain poorly understood. Mainly expressed-sequencetag (EST) libraries of different Trichoderma strains obtained under various growth conditions have contributed significantly to the large-scale identification of active genes (63, 64). Additionally, diverse DNA array experiments have determined that an expansin-like protein, aspartyl proteases, and hydrophobins, among others, are involved in the biocontrol a...