Evidence of small interfering RNA in the fungus Fusarium fujikuroi (RNA-Seq)

RNA interference (RNAi) mechanisms play key regulatory roles in many biological systems, and components of the RNAi pathway are conserved in a wide range of eukaryotic genomes, including those of filamentous fungi. The biotechnological fungus Fusarium fujikuroi, widely used in secondary metabolism studies, contains the complete set of genes expected for RNAi pathways, including dcl1 and dcl2 dicer genes. We have analyzed by means of a high-throughput sequencing technology the content of sRNAs in F. fujikuroi grown in the dark or after one hour of illumination. For comparative purposes, the study was extended to the phytopathogenesis model Fusarium oxysporum, grown under the same conditions. Total RNA samples from each species and growth condition were used to construct RNA libraries, which were subjected to massive sequencing. sRNA preparations included a size cut-off below 150 nt, which covered sRNAs and their precursors. The size distributions and 5' nucleotide preferences of the sRNA reads showed a higher proportion of 5' uracil in the RNA samples of the expected sizes in both species, more noticeable in F. fujikuroi, indicating the occurrence of genuine sRNAs. Consistently, the number of sRNAs mapped at CDS loci was significantly higher in F. fujikuroi compared to F. oxysporum. F. fujikuroi carries at least one transcriptionally expressed copy of a Ty1/copia-like retrotransposable element, in which sRNAs were found in both sense and antisense DNA strands, whereas in F. oxysporum Skippy-like elements are expressed and show siRNA formation. The finding of sRNA in these mobile elements is an indication of an active siRNA-based RNAi pathway. The dcl2 deletion mutants did not show phenotypic alterations or changes in their global transcriptome, while no dcl1 deletion mutants could be obtained. Overall design: This RNA-seq data set investigates the function of the Dicer gene dcl2 in the fungus Fusarium fujikuroi through the effect of its the deletion on the whole transcriptome . The results are presented in a manuscript that provide evidence of the occurrence of smalRNAs in Fusarium and the role of the dcl2 gene by targeted deletion.