Fusarium graminearum (teleomorph Gibberella zeae) is a well known phytopathogenic fungus associated with Fusarium head blight (FHB) disease, which causes blights, root rots, or wilts, especially in economically important cereal crops such as wheat, maize, and barley . FHB is considered an important fungal disease because it drastically reduces grain yield and quality, and produces mycotoxins such as deoxynivalenol (DON) and nivalenol (NIV) in cereals, which are very harmful to human and animal health [2, 3]. The fungus can also infect several dicotyledonous plants including Arabidopsis, tobacco, tomato, and soybean .
Viruses that infect plant fungi are referred to as mycoviruses. Infection by some mycoviruses confers hypovirulence by attenuating pathogenicity to their fungal hosts, which are mostly plant pathogens. Mycoviruses tend to be double-stranded RNA (dsRNA) viruses , and several Fusarium-infecting mycoviruses have been isolated [6–8]. In addition, several whole genome sequences of dsRNA mycoviruses strains derived from F. graminearum have recently been reported [9–12].
In many cases, such as those of F. poae (Fusarium poae virus 1, FpV1)  and F. solani (Fusarium solani virus 1, FsV1), viral infection is not associated with phenotypic changes . However, Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) exhibits interesting phenotypes including reduced mycelial growth and the induction of dark red pigmentation . Several previous studies have provided strong evidence that hypovirulent mycoviruses could be used as substitutes for fungicides [13, 14]. A recent study demonstrated that protoplast fusion is the most efficient approach for transmitting mycoviruses among a wide range of phytopathogenic fungi and that this approach will facilitate the use of mycoviruses as a biocontrol agent .
With the increasing availability of whole genome sequences for representative plant fungal pathogens , extensive and diverse genome-wide analyses can be performed, including transcriptomics, proteomics, and metabolomics . Proteomics approaches for different Fusarium species have enabled examinations of extracellular proteins, proteins involved in fumonisin biosynthesis, and proteome profiles upon antagonistic rhizobacteria inoculation and mycovirus infection [18–21]. Several gene expression analyses based on microarrays have also been conducted [21–25]. For example, genome-wide expression profiling of F. graminearum was carried out to examine responses to treatment with azole fungicide tebuconazole and during perithecium development [22, 24]. Microarrays provide a valuable tool for detecting and identifying Fusarium species that produce specific metabolites such as trichothecene and moniliformin [23, 25]. Moreover, the recently completed genome sequencing of three major Fusarium species provides an important resource for studying pathogenicity and functions of individual genes .
Several microarray-based studies have demonstrated transcriptional changes in fungal genes following mycovirus infection, although most of these studies examined only CHV1-713 infecting the chestnut blight fungus Cryphonectria parasitica. Initially, a polymerase chain reaction (PCR)-based approach demonstrated that elevation of cAMP levels by CHV1-713 resulted in reduced accumulation of the GTP-binding (G) protein subunit CPG-1 . In addition, cDNA microarrays containing 2,200 genes from C. parasitica showed transcriptional change in G-signaling pathways following hypovirus infections showing different virulence or phenotypes [27–29].
Infection by a virus leads to changes in diverse biological processes between fungal host and viral factors. It is of interest to examine such alterations at the molecular level. However, no previous reports have examined expression differences between a fungus containing a mycovirus and an infected parent, aside from two papers that used microarray cDNA chips based on expressed sequence tags to examine fungal host gene expression upon mycovirus infection [28, 29]. Here, we examined genome-wide transcriptional differences in F. graminearum expression between a strain harboring FgV1-DK21 and its uninfected parent. This is the first report of a genome-wide fungal gene expression analysis during mycovirus infection using a 3′ tiling microarray, and our findings show global differences in host cellular pathways in F. graminearum harboring FgV1-DK21.