Research article
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
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* Corresponding author: Erik Kristiansson erik.kristiansson@zool.gu.se
1 Department of Zoology, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
2 Department of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Box 434, SE-405 30 Göteborg, Sweden
BMC Genomics 2009, 10:345 doi:10.1186/1471-2164-10-345
Published: 31 July 2009Abstract
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.