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

Publication date: Available online 20 July 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): D.J. Coughlin, L.K. Nicastro, P.J. Brookes, M.A. Bradley, J.L. Shuman, E.R. Steirer, H.L. MistryAbstractRainbow 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...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - Category: Genetics & Stem Cells Source Type: research