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> Kristiansson Erik 1978
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Characterization of...
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
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- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Zoologiska institutionen, zoofysiologi,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Department of Zoology, Zoophysiology,Institute of Neuroscience and Physiology, Department of Physiology,University of Gothenburg
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- Asker, Noomi, 1968 (author)
- Gothenburg University,Göteborgs universitet,Zoologiska institutionen, zoofysiologi,Department of Zoology, Zoophysiology,University of Gothenburg
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- Förlin, Lars, 1950 (author)
- Gothenburg University,Göteborgs universitet,Zoologiska institutionen, zoofysiologi,Department of Zoology, Zoophysiology,University of Gothenburg
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- Larsson, D. G. Joakim, 1969 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Institute of Neuroscience and Physiology, Department of Physiology,University of Gothenburg
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(creator_code:org_t)
- Springer Science and Business Media LLC, 2009
- 2009
- English.
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10:345
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Abstract
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Industriell bioteknik -- Annan industriell bioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Industrial Biotechnology -- Other Industrial Biotechnology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Farmakologi och toxikologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Pharmacology and Toxicology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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