Abstract
BackgroundThe 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.ResultsHere, 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.ConclusionThe 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.
Highlights
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
We provide a comprehensive annotation of the N. furzeri miRNome based on a combination of Illumina-based small RNA-Seq data, different in silico prediction methods on the genome assembly and a final manual curation
In line with other eukaryotes, we identified multiple gene copies of ribosomal RNA (rRNA), transfer RNA (tRNA), several major spliceosomal RNAs, signal recognition particle (SRP) RNAs and one copy of a minor spliceosomal RNA set
Summary
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. Due to the very short duration of the rainy season in its habitat, the natural lifespan of these animals is limited to a few months. They represent the vertebrate species with the shortest captive lifespan of only 4–12 months and with the fastest maturation. They express a series of conserved aging markers and are amenable to genetic manipulations, making them an attractive model system for aging
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