Magnaporthe oryzae (Mo) is the causal agent of one of the most economically relevant diseases of rice, rice blast, and has been extensively studied as a model Ascomycetes. In addition to colonizing rice aerial parts, Mo is also capable of infecting root tissues and has a wide range of Poaceae hosts, including Brachypodium distachyon(Bd). Recently, it has been suggested that beside protein effectors, fungi produce small (s)RNAs that can be secreted and exchanged with the infected organism in order to silence genes directly associated with the outcome of the infection, a process termed cross-kingdom RNAi (ck-RNA). At the same time, the infection is known to induce sRNA expression in the host, with a subset of them potentially transported to the pathogen to target pathogenicity/virulence genes, resulting in a bidirectional RNAi-based cross-talk between the interacting organisms. In the present work I examined tissue specific mRNA and sRNA expression profiles inMo-Bd interaction in order to characterize the pathosystem and shed further light on thecrucial role that sRNAs play in the establishment and maintenance of fungal infection. By comparative deep sequencing of sRNAs and mRNAs from axenic fungal cultures and infected leaves and roots, I found a wide range of fungal sRNAs that accumulated exclusively in infected tissues. Among those, 20-22 nt candidate sRNAs were predicted in silico by selecting Mo reads that had predicted targets in the Bd transcriptome for a possible cross-kingdom function. Vice versa, we found that during the infection Bd produces sRNAs not only to fulfill an endogenous function, but also to target a variety of fungal transcripts, encoding fungal cell wall components, virulence genes and transcription factors. Consistent with a potential function as effectors, the Bd sRNAs predicted fungal targets were significantly down-regulated in the infected tissues compared to axenic cultures and deletion mutants for some of these target genes are known to result in heavily impaired virulence phenotypes. Overall, this work provides a comprehensive picture of the interaction between rice blast and Bd, both in the transcriptomic reprogramming and the sRNA species produced and potentially exchanged between the pathogenic fungus and its host plant, paving the way for further characterization studies and contributing to the emerging research on naturally occurring cross-kingdom communication and its implications for agriculture.
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