Ekblom Robert, Wennekes Paul, Horsburgh Gavin J, Burke Terry
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.
Mol Ecol Resour. 2014 May;14(3):636-46. doi: 10.1111/1755-0998.12213. Epub 2014 Jan 10.
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.
家麻雀（Passer domesticus）是生态学和进化研究中的重要模式物种。然而，直到最近，该物种仍缺乏用于分子生态项目的基因组资源。在此，我们展示了来自家麻雀三种不同组织（脾脏、血液和法氏囊）的转录组测序数据（RNA测序）。选择这些组织是为了获得表达基因的多样化表征，并最大限度地提高免疫相关基因功能的产量。经过从头组装，鉴定出15250个重叠群，代表了总共8756个已知鸟类基因的序列数据（从亲缘关系密切的斑胸草雀推断而来）。转录组组装包含来自9个手动注释的MHC基因的序列数据，包括一个几乎完整的MHC I类编码序列。在脾脏、血液和法氏囊中分别有407、303和68个基因过表达。与核糖体功能相关的基因本体术语与脾脏中的过表达相关，而与氧运输功能相关的术语与血液中的过表达相关。除了转录序列外，我们还提供了327个具有足够侧翼序列用于引物设计的基因连锁微卫星（SSR），以及基因内的3177个单核苷酸多态性（SNP），可用于对这个经过充分研究的生态物种进行后续的分子生态学研究。
