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To test the hypothesis that gene expression of Trichoderma virens in its beneficial interaction with plants is modulated by the host, we co-cultured T.virens with maize or tomato in a hydroponic system to follow gene expression at the transcript and protein level.The transcriptomes for T.virens alone and with tomato or maize roots were compared by hybridization on oligonucleotide microarrays of 11645 unique probes designed from the predicted protein-coding gene models.The transcript levels of 210 genes were modulated by interaction with roots.