Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data

More Information | Back to archive
Full Text of this article Full article [PDF] (1,07 MB)
doi doi:10.2390/biecoll-jib-2011-169
submission May 01, 2011
last revision August 15, 2011
published September 12, 2011
NCBI PubMed PubMed ID 21908900

Yanju Zhang, Elia Stupka, Christiaan V. Henkel, Hans J. Jansen, Herman P. Spaink and Fons J. Verbeek

Correspondence should be addressed to:
Yanju Zhang
Section Imaging and BioInformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, The Netherlands
ln.scail@nullujnay


Abstract

The common carp is a candidate model system for immunology research. Using next-generation sequencing technology, we have generated a huge amount of sequence reads from the carp genome and transcriptome. Currently, our aim is to identify carp genes involved in the development of the innate immune response, particularly TIR domain-containing genes, from a preliminary genome assembly. To achieve this, we developed a comprehensive gene identification pipeline. This analysis allowed us to estimate that the carp has 39 TIR domain-containing transcript isoforms and genes.

Reference

Yanju Zhang, Elia Stupka, Christiaan V. Henkel, Hans J. Jansen, Herman P. Spaink and Fons J. Verbeek. Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data. Journal of Integrative Bioinformatics, 8(2):169, 2011. Online Journal: http://journal.imbio.de/index.php?paper_id=169
imprint | sitemap | credits | top