title: Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics.
abstract: The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15,250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.
authors.affiliation: Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, SE-75236, Sweden; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Ekblom
authors.forename: Paul
authors.initials: P
authors.lastname: Wennekes
authors.forename: Gavin J
authors.initials: GJ
authors.lastname: Horsburgh
authors.forename: Terry
authors.initials: T
authors.lastname: Burke
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D004463:Ecology; D006649:Histocompatibility Antigens / Q000235:genetics; D007125:Immunogenetics; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D046370:Sparrows / Q000145:classification / Q000235:genetics* / Q000276:immunology; D059467:Transcriptome
chemical_list: D030161:Avian Proteins; D006649:Histocompatibility Antigens
keywords: MHC; RNA-Seq; SNP; bird; microsatellite; transcriptome