Meeting Abstract
Rainbow smelt, Osmerus mordax, have an impressive ability to acclimate to very cold water. Smelt exposed to cold for an extended period of time have faster sustained swimming speeds and increased contraction kinetics in their myotomal muscle compared to warm acclimated fish. We used RNA-Seq to explore how gene expression underlies thermal acclimation in these fish. Transcriptome analysis is limited in species that lack an annotated genome, such as rainbow smelt. The Trinity software package (Broad Institute) permits the de novo assembly of a smelt transcriptome with a modest learning curve. The workflow was extended with Kallisto to quantify the abundance of each transcript represented in the full transcriptome and Sleuth to analyze the resulting RNA-seq datasets. Subsequently qPCR can be used to confirm patterns of thermal acclimation and gene expression for gene of metabolic and muscle contractile function. This approach has proven fruitful in revealing the genes responsible for the increase in physiological performance in over-wintering smelt.
