miRCandRef (microRNA-candidate-reference) for microRNA predictions for non-genome organisms

Recent studies on microRNA evolution focused mainly on the comparison of microRNA complements between animal clades. However, evolution of microRNAs within such groups is poorly explored despite the availability of comparable data that in some cases lack only a few key taxa. For flatworms (Platyhelminthes) microRNA complements are available for some free-living flatworms and all major parasitic lineages, except for the Monogenea.

Now researchers from the University of Oslo, Norway present the microRNA complement of the monogenean flatworm Gyrodactylus salaris that facilitates a comprehensive analysis of microRNA evolution in Platyhelminthes. Using the newly designed bioinformatics pipeline miRCandRef the microRNA complement was disentangled from Next-Generation-Sequencing of smallRNAs and genomic DNA without a priori genome-assembly. It consists of 39 microRNA hairpin loci of conserved microRNA families, and 22 novel microRNAs.


The bioinformatics pipeline miRCandRef (microRNA-candidate-reference) was developed to enable miRNA predictions for non-genome organisms like G. salaris. Briefly, miRCandRef uses genomic and smallRNA data from Next-Generation-Sequencing (NGS) and locally assembles genomic reads that match microRNA candidates from smallRNA-reads into relatively short genomic contigs (crystal-contigs). MiRCandRef delivers a multi-fasta file of assembled and clustered miRNA crystal-contigs that can be used as a genomic reference for miRNA prediction software rather than a properly assembled genome. Using this approach allows for a comparably fast miRNA prediction directly from NGS reads and circumvents the need for costly and sometimes patchy draft genome-assemblies.

In its current version the pipeline includes a modified version of miRDeep2 (Friedländer, et al. 2011) that can handle the miRCandRef-fastaoutput files and smallRNA reads for miRNA-prediction. To simplify the usage of the pipeline, miRCandRef has been implemented at the latest version of the hyperbrowser (http://hyperbrowser.uio.no) (Sandve, et al. 2013), which is based on the Galaxy system (Giardine, et al. 2005) and allows for a fully automated analysis based on smallRNA and DNA-reads uploaded by the user.

  • Fromm B, Worren MM, Hahn C, Hovig E, Bachmann L. (2013) Substantial loss of conserved and gain of novel microRNA families in flatworms. Mol Biol Evol [Epub ahead of print]. [article]