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Background  The short-lived fish  Nothobranchius furzeri  is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression.    Results  Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for  Nothobranchius furzeri . Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven  Nothobranchius  species. Additionally, duplication and clustering of  N. furzeri  miRNAs was analyzed and compared to the four fish species  Danio rerio ,  Oryzias latipes ,  Gasterosteus aculeatus  and  Takifugu rubripes . A peculiar characteristic of  N. furzeri , as compared to other teleosts, was a duplication of the miR-29 cluster.    Conclusion  The completeness of the catalogue we provide is comparable to that of the zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3951-8) contains supplementary material, which is available to authorized users.

A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri