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Background  Accumulating evidence demonstrates that non-coding RNAs (ncRNAs) are indispensable components of many organisms and play important roles in cellular events, regulation, and development.    Results  Here, we analysed the small non-coding RNA (ncRNA) transcriptome of  Trichophyton rubrum  by constructing and sequencing a cDNA library from conidia and mycelia. We identified 352 ncRNAs and their corresponding genomic loci. These ncRNA candidates included 198 entirely novel ncRNAs and 154 known ncRNAs classified as snRNAs, snoRNAs and other known ncRNAs. Further bioinformatic analysis detected 96 snoRNAs, including 56 snoRNAs that had been annotated in other organisms and 40 novel snoRNAs. All snoRNAs belonged to two major classes—C/D box snoRNAs and H/ACA snoRNAs—and their potential target sites in rRNAs and snRNAs were predicted. To analyse the evolutionary conservation of the ncRNAs in  T. rubrum , we aligned all 352 ncRNAs to the genomes of six dermatophytes and to the NCBI non-redundant nucleotide database (NT). The results showed that most of the identified snRNAs were conserved in dermatophytes. Of the 352 ncRNAs, 102 also had genomic loci in other dermatophytes, and 27 were dermatophyte-specific.    Conclusions  Our systematic analysis may provide important clues to the function and evolution of ncRNAs in  T. rubrum . These results also provide important information to complement the current annotation of the  T. rubrum  genome, which primarily comprises protein-coding genes.

Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum