Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Artikel i vetenskaplig tidskrift, 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.

Författare

Erik Kristiansson

Göteborgs universitet

Noomi Asker

Göteborgs universitet

Lars Förlin

Göteborgs universitet

D. G. Joakim Larsson

Göteborgs universitet

BMC Genomics

1471-2164 (ISSN)

Vol. 10 345

Ämneskategorier

Biokemi och molekylärbiologi

Farmakologi och toxikologi

Bioinformatik och systembiologi

Genetik

Annan industriell bioteknik

DOI

10.1186/1471-2164-10-345

Mer information

Skapat

2017-10-10