ted, the direction of expression was confirmed by Q-PCR for 7 contigs: 4 up-regulated and 3 down-regulated; whereas the expression of 3 contigs was different between the two methods. Discussion In this study, we have performed RNA-seq to provide an in-depth view, for the first time, of the transcriptome of skeletal muscle of the rainbow trout, a commercially important species still without a sequenced genome. In particular, we have sequenced and compared the red and white muscle transcriptome and have used RNA-seq for the quantification of the effects of exercise in the rainbow trout skeletal muscle. Importantly, novel rainbow trout gene sequences have been identified in this study: 1,085 gene sequences in red muscle and 1,228 gene sequences in white muscle. Applying RNA-seq to Identify Genes Expressed in Rainbow Trout Skeletal Muscle and to Measure Changes in the Red and White Muscle Transcriptomes in Response to Exercise De novo assembly of reads into contigs per tissue was performed at efficiencies between 42.1 and 45.3%. Efficiencies were thus rather low and more than half of the reads had to be discarded. Most contigs were small in the absence of a sequenced rainbow trout genome, with 79% of the red muscle contigs and 73% of the white muscle contigs having lengths between 100 and 200 nt. Annotation efficiencies obtained by the three-step iterative homology search approach used in this study were 44.3% for the red muscle contigs and 51.8% for the white muscle contigs. These annotation efficiencies were acceptable, especially when taking into account the absence of a sequenced trout genome, and are comparable to other RNA-seq transcriptomic studies. The SIGENAE salmonid EST database provided,70% of the BLAST hits. Annotation efficiencies of the large contigs were,70% and approached those reported for zebrafish. One of the most important findings of this study is the identification of a number of novel rainbow trout gene sequences in red and in white muscle by a homology search strategy against the zebrafish genome and general Metazoan genes. In total, we have identified 1,432 novel rainbow trout sequences but among these, however, there were many hypothetical, probable and predicted protein sequences. When these unannotated sequences were filtered out of the results, 731 novel rainbow trout annotated sequences remained. Among this novel set of rainbow trout sequences, we have identified important growth and myogenic factors and their receptors that participate in the regulation of myogenic proliferation and differentiation, such as myocyte enhancer factor 2C, myogenic factor 6, fibroblast growth factor 1, follistatin-like 1b, heparinbinding EGF-like 
growth factor, TGF-beta receptor type-2, bone morphogenetic protein receptor, type 14530216 1a and leukemia inhibitory Deep RNA Sequencing of Trout Muscle factor receptor alpha. Of particular interest is the identification of Wnt-2 and its receptor Frizzled homolog 3-like, MedChemExpress Ancitabine (hydrochloride) components of the Wnt pathway that has been associated with skeletal muscle development and with adult muscle hypertrophy induced by mechanical overload in mammals. In addition, components of the insulin-like growth factor family were identified, including 15771452 the cation-independent mannose-6-phosphate receptor or IGF-2 receptor, known to transduce the myogenic differentiation-promoting effects of IGF-2 in muscle, and several IGF binding proteins that regulate the biological activity of IGF-1. Interestingly, there is also evidence f
