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Background   Trichoderma  spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind  Trichoderma -derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes  Trichoderma  utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by  T. virens  during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex.    Results  We present a model of  T. virens  – maize interaction wherein  T. virens  experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots,  T. virens  modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of  T. virens  activity in maize roots.    Conclusions   T. virens  displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of  T. virens  as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering  T. virens  – maize symbiosis.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5651-z) contains supplementary material, which is available to authorized users.

Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots