Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

Andreas Petzold1*, Kathrin Reichwald1, Marco Groth1, Stefan Taudien1, Nils Hartmann2, Steffen Priebe3, Dmitry Shagin45, Christoph Englert2 and Matthias Platzer1

Author Affiliations

1 Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr. 11, Jena 07745, Germany

2 Molecular Genetics, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr. 11, Jena 07745, Germany

3 Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstr. 11a, Jena 07745, Germany

4 Evrogen Ru SJC, Milukho-Maklaya 16/10, Moscow 117997, Russia

5 Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Milukho-Maklaya 16/10, Moscow 117997, Russia

For all author emails, please log on.

BMC Genomics 2013, 14:185  doi:10.1186/1471-2164-14-185

Published: 16 March 2013

Abstract

Background

The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.

Results

To build the N. furzeri transcript catalogue, thirteen cDNA libraries were sequenced using Sanger, 454/Roche and Solexa/Illumina technologies yielding about 39 Gb. In total, 19,875 protein-coding genes were identified and annotated. Of these, 71% are represented by at least one transcript contig with a complete coding sequence. Further, transcript levels of young and old fish of the strains GRZ and MZM-0403, which differ in lifespan by twofold, were studied by RNA-seq. In skin and brain, 85 differentially expressed genes were detected; these have a role in cell cycle control and proliferation, inflammation and tissue maintenance. An RNA-seq experiment for zebrafish skin confirmed the ageing-related relevance of the findings in N. furzeri. Notably, analyses of transcript levels between zebrafish and N. furzeri but also between N. furzeri strains differed largely, suggesting that ageing is accelerated in the short-lived N. furzeri strain GRZ compared to the longer-lived strain MZM-0403.

Conclusions

We provide a comprehensive, annotated N. furzeri transcript catalogue and a first transcriptome-wide insight into N. furzeri ageing. This data will serve as a basis for future functional studies of ageing-related genes.

Keywords:
Nothobranchius furzeri; Model fish species; Ageing; Transcriptome assembly; Transcript catalogue; Gene expression; RNA-seq