Genome-wide analysis of small RNAs in the wheat pathogenic fungus Zymoseptoria tritici.

Small non-coding RNAs constitute a large family of regulatory molecules with diverse function. Knowledge about small RNAs in fungi remains limited. Here, a RNA-seq-based analysis of small RNA transcriptome from the wheat pathogenic fungus Zymoseptoria tritici under nutrient-stress and nutrient-rich growth conditions is presented. Small RNAs mapped to Z. tritici genomic features including sense and antisense strands of genes, repetitive elements, rRNAs, snRNA, snoRNA and tRNA loci throughout the chromosomes. The majority of small RNAs from rich condition mapped to all the chromosomes, primarily the sense strand of chromosome seven, but under stress condition, small RNAs were enriched in accessory genome. Inspection of the predominant small RNAs matching to protein-coding genes, repeats and rRNAs revealed that intron and LTP retrotransposon-derived small RNAs accumulated upon stress, whereas rRNA-derived small RNAs were enriched for nutrient-rich condition. U enrichment at position 1 of small RNAs mapping to repeats and antisense-strand genes was only observed from stress library. Additionally, target analysis of one predicted milRNA suggests its potential role in fungal pathogenesis and manipulation of host immunity. Taken together, the findings provide a new insight into the function of small RNAs in regulating growth and development, stress adaptation, and possibly pathogenesis in Z. tritici.