The recently sequenced Sebacina vermifera (MAFF 305830) is a root endophyte with wide-host spectrum beneficial effects while Bipolaris sorokiniana (ND90Pr) is a serious root pathogen for barley. Recent studies showed that S. vermifera is able to increase resistance of barley to B. Sorokiniana, suggesting a possible function in biological control. Transcriptional profile of multipartite fungus-plant interactions in split-root experiment was generated. The RNA-Seq data was analysed to determine systemic and local interaction of mutualistic and pathogenic fungi in barley roots.