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

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

Published: 16 March 2013

Additional files

Additional file 1: Table S1:

BLAST parameter adapted from [55].

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Additional file 2: Figure S1:

Functional annotation based on Gene Ontology. Second level GO-Slim terms for the longest transcripts per N. furzeri gene in the three domains: A) biological process, B) molecular function and C) cellular component.

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Additional file 3: Figure S2:

BLAST analysis of N. furzeri transcript contigs vs. proteins of medaka, stickleback, tetraodon and zebrafish. Venn diagram showing 96,106 (46%) N. furzeri transcript contigs with BLASTx hits to Ensembl protein annotations of the four fish genomes. A set of 73,238 transcript contigs (35%) had hits in all four fish species, whereas 8,175 transcript contigs (4%) representing a total of 2,489 genes had hits exclusively in one species.

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Additional file 4:

Genes duplicated in N. furzeri. List of duplicated genes identified in the N. furzeri transcript catalogue.

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Additional file 5: Figure S3:

NFINtb N. furzeri transcriptome browser. To provide easy access, the Nothobranchius furzeri Information Network transcriptome browser was installed. The screenshot shows the query page, which is used to search transcript contigs by keywords (e.g. annotation, gene symbol, GO category).

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Additional file 6:

N. furzeri ageing-related genes in skin and brain. Lists of differentially expressed genes in skin and brain of N. furzeri detected by RNA-seq.

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Additional file 7:

Enriched functional annotation terms obtained for N. furzeri ageing-related genes. Enriched functional annotation terms obtained by DAVID for up- and downregulated genes as well as for skin- and brain-specific genes that were differentially expressed in N. furzeri with age.

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Additional file 8: Table S2:

Primer sequences for qRT-PCR validation of RNA-seq results of selected N. furzeri ageing-related genes.

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Additional file 9:

N. furzeri ageing-related genes in skin and their confirmation in zebrafish. Lists of N. furzeri differentially expressed genes in skin and their confirmation in skin of old vs. young zebrafish.

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