UBC Research Data

Data from: Similarities in temperature-dependent gene expression plasticity across time-scales in threespine stickleback (Gasterosteus aculeatus) Metzger, David C.H.; Schulte, Patricia M.; Metzger, David C. H.

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Abstract
Phenotypic plasticity occurs at a variety of time-scales, but little is known about the degree to which plastic responses at different time-scales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we identified differential gene expression in response to developmental temperature in the muscle transcriptome of adult threespine stickleback (Gasterosteus aculeatus) exposed to 12, 18, and 24 °C until hatch and then held at 18 °C for nine months, and compared these results to differential gene expression in response to adult thermal acclimation in stickleback developed at 18 °C and then acclimated to 5 and 25 °C as adults. Adult thermal acclimation affected the expression of 7,940 and 7,015 genes in response to cold and warm acclimation, respectively, and 4,851 of these genes responded in both treatments. In contrast, the expression of only 33 and 29 genes were affected by cold and warm development, respectively. The majority of the genes affected by developmental temperature were also affected by adult acclimation temperature. Many genes that were differentially expressed as a result of adult acclimation were associated with previously identified temperature-dependent effects on DNA methylation patterns, suggesting a role of epigenetic mechanisms in regulating gene expression plasticity during acclimation. Taken together, these results demonstrate similarities between the persistent effects of developmental plasticity on gene expression and the effects of adult thermal acclimation, emphasizing the potential for mechanistic links between plasticity acting at these different life stages.; Usage notes
Total_Read_Counts_Thermal_AcclimationRNA-seq read count data for muscle tissue of threespine stickleback individuals reared at 18 degrees Celsius from fertilization until adults and then acclimated to 5, 18, or 25 degrees Celsius for four weeks.ATreadcounts.csv
Total_Read_Counts_Developmental_TemperatureRNA-seq read count data for muscle tissue of threespine stickleback individuals reared at either 12, 18, or 24 degrees Celsius from fertilization until hatch. All individuals were then kept at 18 degrees Celsius until muscle tissue samples were taken as adults.DTreadcounts.csv
R script for RNA-seq analysis of thermal acclimation read countsR code used for RNA-seq analysis of the thermal acclimation read count data . All read count data files used in this analyses can be found in the additional files associated with this Dryad submission.AccTempRNAseqRscript.txt
R script for RNA-seq analysis of developmental temperature read countsR code used for RNA-seq analysis of the developmental temperature read count data . All read count data files used in this analyses can be found in the additional files associated with this Dryad submission.DevTempRNAseqRscript.txt

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