Research

High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

Kathrin Reichwald¹ , Chris Lauber^1,4 , Indrajit Nanda^2,3 , Jeanette Kirschner¹ , Nils Hartmann¹ , Susanne Schories² , Ulrike Gausmann¹ , Stefan Taudien¹ , Markus B Schilhabel^1,5 , Karol Szafranski¹ , Gernot Glöckner¹ , Michael Schmid³ , Alessandro Cellerino¹ , Manfred Schartl² , Christoph Englert¹ and Matthias Platzer¹

¹  Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr., 07745 Jena, Germany

²  Department of Physiological Chemistry I, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany

³  Department of Human Genetics, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany

⁴  Current address: Department of Medical Microbiology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands

⁵  Current address: Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstr., 24105 Kiel, Germany

author email corresponding author email

Genome Biology 2009, 10:R16doi:10.1186/gb-2009-10-2-r16

Published:	11 February 2009

Subject areas: Genome studies, Medicine

Abstract

Background

The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research.

Results

To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred.

Conclusions

Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.