Thermal acclimation and gene expression in rainbow smelt: Changes in the myotomal transcriptome in the cold

Rainbow smelt, Osmerus mordax, have an impressive ability to acclimate to very cold water. Rainbow smelt exposed to cold (<5 °C) 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 Sequencing reactions (RNA-Seq) to explore how gene expression underlies thermal acclimation by muscle in these fish. Transcriptome analysis is limited in species that lack an annotated genome, such as rainbow smelt. The Trinity software package permits the de novo assembly of a rainbow smelt transcriptome with a modest learning curve. The transcriptome was then analyzed 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 was used to explore patterns of thermal acclimation and gene expression for genes of metabolic and muscle contractile function. These methodologies revealed shifts in both muscle and metabolic gene expression that contribute to the thermal acclimation response in rainbow smelt. In fast-twitch, anaerobic white muscle, slow isoforms of myosin heavy and light chain tended to be down-regulated with exposure to cold in myotomal muscle, while fast isoforms were unchanged. Genes associated with protein turnover and aerobic metabolism were up-regulated in the white muscle, while those associated with anaerobic metabolism and the cell cycle were down-regulated. Collectively the results suggest that thermal acclimation to cold is complex process of apparent shifts in gene expression.