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

BMC Genomics

Research Article

Dmitry Shagin¹  Andreas Petzold²  Marco Groth²  Matthias Platzer²  Stefan Taudien²  Kathrin Reichwald²  Nils Hartmann³  Christoph Englert³  Steffen Priebe⁴ 

[1] Evrogen Ru SJC, Milukho-Maklaya 16/10, 117997, Moscow, Russia;Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Milukho-Maklaya 16/10, 117997, Moscow, Russia;Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany;Molecular Genetics, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany;Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstr. 11a, 07745, Jena, Germany;

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

DOI  :  10.1186/1471-2164-14-185

 received in 2012-07-19, accepted in 2013-03-05,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsTo 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.ConclusionsWe 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.

【 授权许可】

CC BY   
© Petzold et al.; licensee BioMed Central Ltd. 2013