title: Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.
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.
authors: Section Imaging and BioInformatics, Leiden Institute of Advanced Computer Science(LIACS), Leiden University, The Netherlands. yanju@liacs.nl
authors: Yanju
authors: Y
authors: Zhang
authors: Elia
authors: E
authors: Stupka
authors: Christiaan V
authors: CV
authors: Henkel
authors: Hans J
authors: HJ
authors: Jansen
authors: Herman P
authors: HP
authors: Spaink
authors: Fons J
authors: FJ
authors: Verbeek
mesh_terms: D000818:Animals; D001483:Base Sequence; D002347:Carps / Q000235:genetics* / Q000276:immunology*; D016678:Genome / Q000235:genetics*; D006720:Homozygote; D007113:Immunity, Innate / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017434:Protein Structure, Tertiary; D012313:RNA / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D015027:Zebrafish / Q000235:genetics; D029961:Zebrafish Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D029961:Zebrafish Proteins; D012313:RNA