A Naturally Occurring Defective RNA Species of the Tymo-Like Mycovirus FbLFV1 Confers Hypovirulence in the Host Fusarium Head Blight Fungus, Fusarium boothii

RNA viruses often generate a defective RNA (D-RNA) species that has internal deletion(s) and recombined fragment(s), which are believed to occur during viral replication. Such subviral RNA fragments sometimes exert overt effects on their parental viral replication or pathogenicity and are called defective-interfering RNA (DI-RNA). This study reports a rare example in which a D-RNA acquired a novel function that determines the hypovirulent phenotype of the host fungus, Fusarium boothii Ep-BL13, a causal agent of Fusarium head blight. The parental Fusarium boothii large flexivirus 1 (FbLFV1) is a tymo-like virus with a 13 kb (+)ssRNA genome encoding a single large ORF, and the D-RNA has an approximately 10 kb internal deletion in the ORF with an in-frame connection. Partial virus curing revealed a clear association between viral infection (FbLFV1 + D-RNA) and inhibition of colony growth and the pathogenicity of the host F. boothii. These traits were further confirmed in a fungal strain expressing the D-RNA ORF, specifically under FbLFV1 infection. Moreover, FbLFV1 and D-RNA infection decreased the host fungal production of the mycotoxin deoxynivalenol. Overall, FbLFV1 produced a D-RNA in F. boothii in nature, which carries the rearranged gene (D-RNA ORF) with a virulence-determining function, representing a rare example of gain-of-function by a D-RNA.