Fox Samuel E, Christie Mark R, Marine Melanie, Priest Henry D, Mockler Todd C, Blouin Michael S
Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Department of Zoology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Mar Genomics. 2014 Jun;15:13-5. doi: 10.1016/j.margen.2013.12.001. Epub 2014 Jan 17.
Identifying the traits that differ between hatchery and wild fish may allow for pragmatic changes to hatchery practice. To meet those ends, we sequenced, assembled, and characterized the anadromous steelhead (Oncorhynchus mykiss) transcriptome. Using the Illumina sequencing platform, we sequenced nearly 41million 76-mer reads representing 3.1 Gbp of steelhead transcriptome. Upon final assembly, this sequence data yielded 86,402 transcript scaffolds, of which, 66,530 (77%) displayed homology to proteins of the non-redundant NCBI database. Gene descriptions and gene ontology terms were used to annotate the transcriptome resulting in 4030 unique gene ontology (GO) annotations attributed to the assembled sequences. We also conducted a comparative analysis that identified homologous genes within four other fish species including zebrafish (Danio rerio), stickleback (Gasterosteus aculeatus), and two pufferfish species (Tetraodon nigroviridis and Takifugu rubripes). Comparing our steelhead reference assembly directly to the transcriptome for rainbow trout (the fresh water life-history variant of the same species) revealed that while the steelhead and rainbow trout transcriptomes are complementary, the steelhead data will be useful for investigating questions related to anadromous (ocean-going) fishes. These sequence data and web tools provide a useful set of resources for salmonid researchers and the broader genomics community (available at http://salmon.cgrb.oregonstate.edu).
识别孵化场养殖的鱼和野生鱼之间的差异特征，可能会使孵化场的养殖实践发生切实可行的变化。为了实现这些目标，我们对溯河洄游的虹鳟（Oncorhynchus mykiss）转录组进行了测序、组装和特征分析。利用Illumina测序平台，我们对近4100万个76碱基对的读段进行了测序，这些读段代表了3.1千兆碱基对的虹鳟转录组。最终组装后，这些序列数据产生了86402个转录本支架，其中66530个（77%）与非冗余NCBI数据库中的蛋白质具有同源性。使用基因描述和基因本体术语对转录组进行注释，最终为组装序列赋予了4030个独特的基因本体（GO）注释。我们还进行了一项比较分析，在包括斑马鱼（Danio rerio）、棘鱼（Gasterosteus aculeatus）以及两种河豚（Tetraodon nigroviridis和Takifugu rubripes）在内的其他四种鱼类中鉴定出同源基因。将我们的虹鳟参考组装与虹鳟（同一物种的淡水生活史变种）的转录组直接比较后发现，虽然虹鳟和虹鳟转录组是互补的，但虹鳟数据将有助于研究与溯河洄游（海洋洄游）鱼类相关的问题。这些序列数据和网络工具为鲑科鱼类研究人员和更广泛的基因组学群体提供了一套有用的资源（可在http://salmon.cgrb.oregonstate.edu获取）。
