The fungal pathogen Fusarium graminearum infect both heads and roots of cereal crops causing several economically important diseases such as head blight, seedling blight, crown rot and root rot. Trichothecene mycotoxins such as deoxynivalenol (DON), a well-known virulence factor, produced by F. graminearum (Fg) during disease development is also an important health concern. Although how F. graminearum infects above-ground tissues is relatively well studied, very little is known about molecular

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... rocesses employed by the pathogen during below-ground infection. Also unknown is the role of DON during root infection. In the present study, we analyzed the transcriptome of F. graminearum during root infection of the model cereal Brachypodium distachyon. We also compared our Fg transcriptome data during root infection with those reported during wheat head infection. These analyses suggested that both shared and unique infection strategies employed by the pathogen during colonization of different host tissues. Several metabolite biosynthesis genes induced in F. graminearum during root infection could be linked to phytohormone production, implying that the pathogen likely interferes root specific defenses. In addition, to understand the role of DON in Fg root infection, we analyzed the transcriptome of the DON deficient Tri5 mutant. These analyses showed that the absence of DON had a significant effect on fungal transcriptional responses. Although DON was produced in infected roots, this mycotoxin did not act as a virulence factor during root infection. Our results reveal new mechanistic insights into the below-ground strategies employed by F. graminearum that may benefit the development of new genetic tools to combat this important cereal pathogen.