The mTOR inhibitor first-pass assembly was performed with Velvet and ABySS to assemble short contigs using both our Illumina reads and available ESTs ( Simpson et al., 2009 and Zerbino
and Birney, 2008). Second-pass assembly was completed with the MIRA assembler to combine Velvet and ABySS contigs, steelhead Illumina reads, and tentative consensus transcripts into longer transcript scaffolds ( Chevreux et al., 1999). A total of 86,157 transcript scaffolds were greater than 100 bp with an average length of 902 bp (Fig. 1; Supplementary file 1). We assembled 27,095 transcript scaffolds greater than 1 kb averaging 1509 bp. Of the 86,402 transcript scaffolds, 49,149 homologous genes were identified using E-value cutoff of 10− 5. We assigned GO terms to each sequence using the Blast2GO tools (Supplementary file 2; Gotz et al., 2008). A total of 4030 gene ontology definitions were identified among the group of 24,624 transcript scaffolds. The biological processes class was the most highly Sotrastaurin mw represented (68.3%), followed by molecular function (22.2%) and cellular component (9.5%; Fig. 1). See Supplementary Methods for more details regarding functional annotation. The top BLASTx hits to other fishes included
zebrafish (Danio rerio), Atlantic salmon (Salmo salar), and pufferfish (Tetraodon nigroviridis and Takifugu rubripes) ( Fig. 2). In addition, we conducted comparisons between the rainbow trout/steelhead assemblies and zebrafish proteins ( Fig. 2;
See Supplementary Methods for details). The O. mykiss raw sequence data from this study is accessioned in the NCBI Sequence Read Archive (SRA accession SRP009644.1). We have also made a searchable BLAST database to facilitate research using aminophylline steelhead trout (http://salmon.cgrb.oregonstate.edu/). All transcriptome reference contigs, predicted proteins, and associated GO terms are available via FTP on the Salmon Resource website. The following are the supplementary data related to this article. Supplementary Methods. We thank the Oregon Department of Fish and Wildlife for their assistance in collecting the hatchery and wild steelhead trout, and staff of the Parkdale and Oak Springs hatchery for crossing and raising the fish, in particular, Jim Gidley and Lyle Curtis. We are grateful to Anne-Marie Girard and Caprice Rosato for the qualitative assessment of RNA and cDNA and Mark Dasenko (Center for Gene Research and Biocomputing, Oregon State University) for Illumina cluster generation and sequencing. We thank Matthew Peterson and especially Chris Sullivan (Center for Gene Research and Biocomputing, Oregon State University) for computational support. “
“By virtue of their abundance, surface area and metabolic versatility, microbes mediate the vast majority of organic matter transformations in the ocean and control the flow of energy and key nutrients (C, N, P, S, Fe) to higher trophic levels (Falkowski et al., 2008).