Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Journal article, 2009

Background The teleost Zoarces viviparus (eelpout) lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this species genome has however restrained the use of efficient molecular-level assays, such as gene expression microarrays. Results In the present study we present the first comprehensive characterization of the Zoarces viviparus liver transcriptome. From 400,000 reads generated by massively parallel pyrosequencing, more than 50,000 pieces of putative transcripts were assembled, annotated and functionally classified. The data was estimated to cover roughly 40% of the total transcriptome and homologues for about half of the genes of Gasterosteus aculeatus (stickleback) were identified. The sequence data was consequently used to design an oligonucleotide microarray for large-scale gene expression analysis. Conclusion Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates enough genomic information for adequate de novo assembly of a large number of genes in a higher vertebrate. The generated sequence data, including the validated microarray probes, are publicly available to promote genome-wide research in Zoarces viviparus.

Author

Erik Kristiansson

University of Gothenburg

Noomi Asker

University of Gothenburg

Lars Förlin

University of Gothenburg

D. G. Joakim Larsson

University of Gothenburg

BMC Genomics

1471-2164 (ISSN)

Vol. 10 345

Subject Categories

Biochemistry and Molecular Biology

Pharmacology and Toxicology

Bioinformatics and Systems Biology

Genetics

Other Industrial Biotechnology

DOI

10.1186/1471-2164-10-345

More information

Created

10/10/2017