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BMC Genomics. 2017 Sep 5;18(1):693. doi: 10.1186/s12864-017-3951-8.

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

Author information

1
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
2
Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany.
3
Babraham Institute, Cambridge, England.
4
Dresden University of Technology, Dresden, Germany.
5
European Brain Research Institute (EBRI), Rome, Italy.
6
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany. manja@uni-jena.de.
7
Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany. manja@uni-jena.de.
8
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany. alessandro.cellerino@sns.it.
9
Laboratory of Biology, Scuola Normale Superiore, 56126, Pisa, Italy. alessandro.cellerino@sns.it.

Abstract

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.

KEYWORDS:

Fish miRNA evolution; Nothobranchius furzeri; miRNome; ncRNA

PMID:
28874118
PMCID:
PMC5584509
DOI:
10.1186/s12864-017-3951-8
[Indexed for MEDLINE]
Free PMC Article

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