Fusarium solani genome sequencing, assembly, transcriptome and small RNA sequencing

A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and their pathogens. Mobile RNAi signals translocate from plants to pathogenic fungi and vice versa, to establish bi-directional cross-kingdom RNAi to the advantage of either the host or the pathogen, respectively. Whether similar RNAi-based mechanisms govern the communication of plants with non-pathogenic symbiotic microorganisms has been elusive to this date. The soil-borne beneficial fungal endophyte Fusarium solani strain K (FsK) confers resistance and/or tolerance to biotic and abiotic stress in tomato and, as shown in this study, promotes plant growth in Nicotiana benthamiana. Characterizing its core RNAi machinery, we determined that FsK encodes two Dicer-like (DCL) endonucleases, 2 Argonaute (AGO) proteins and 4 RNA-dependent RNA (RDR) polymerases. FsK DCLs process endogenously-transcribed or exogenously-applied double stranded RNAs (dsRNAs) into short interfering RNAs (siRNAs) which lead to the degradation of homologous mRNAs. However, no RDR-mediated transitivity on the targeted mRNA or RNA-directed DNA methylation (RdDM) on the cognate DNA takes place in the fungus. Importantly, we provide evidence that FsK colonization of N. benthamiana led to the induction of systemic silencing and RdDM of a host reporter gene. These data may reflect a more general but so far unrecognized mechanism wherein fungal endophytes translocate RNAi signals to its hosts to modulate gene expression during symbiosis.