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).
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