The conidium plays a critical role in the life cycle of many filamentous fungi, being the primary means for survival under unfavorable conditions. To investigate the transcriptional changes taking place during the transition from growing hyphae to conidia in Trichoderma reesei, microarray experiments were performed. A total of 900 distinct genes were classified as differentially expressed, relative to their expression at time zero of conidiation, at least at one of the time points analyzed. The main functional categories (FunCat) overrepresented among the upregulated genes were those involving solute transport, metabolism, transcriptional regulation, secondary metabolite synthesis, lipases, proteases, and, particularly, cellulases and hemicellulases. Categories overrepresented among the downregulated genes were especially those associated with ribosomal and mitochondrial functions. The upregulation of cellulase and hemicellulase genes was dependent on the function of the positive transcriptional regulator XYR1, but XYR1 exerted no influence on conidiation itself. At least 20% of the significantly regulated genes were nonrandomly distributed within the T. reesei genome, suggesting an epigenetic component in the regulation of conidiation. The significant upregulation of cellulases and hemicellulases during this process, and thus cellulase and hemicellulase content in the spores of T. reesei, contributes to the hypothesis that the ability to hydrolyze plant biomass is a major trait of this fungus enabling it to break dormancy and reinitiate vegetative growth after a period of facing unfavorable conditions. Differentiation into a dormant resting stage (most frequently called "spores") has been developed by a broad variety of prokaryotic and eukaryotic organisms to survive long periods of environmentally unfavorable conditions (19,38). For a diverse group of fungi that includes many medically, industrially, and agriculturally important species, conidiation is also a common asexual reproductive mode and primary means for dispersion in the environment. It involves major rearrangements of many fundamental growth and cell cycle processes (including temporal and spatial regulation of gene expression, cell specialization, and intercellular communication) (13,17,37).The genetic mechanisms controlling these processes in fungi have been addressed in some detail for only two well-studied ascomycetes, Aspergillus nidulans and Neurospora crassa, which, despite displaying similar general mechanisms, revealed significant differences (2, 10, 13, 47). A common feature of fungal spores from both species, however, is their content of a high number of RNAs that can be rapidly translated at the very beginning of germination, thus minimizing the time and energy needed to initiate growth once a suitable substrate becomes available.The filamentous fungus Trichoderma reesei (the anamorph of the pantropical ascomycete Hypocrea jecorina [28]) is intensively investigated because of its ability to produce plant biomass-hydrolyzing enzyme mixtur...