Data from: Similarities in temperature-dependent gene expression plasticity across time-scales in threespine stickleback (Gasterosteus aculeatus)

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.

表型可塑性（Phenotypic plasticity）可在多种时间尺度上发生，但目前学界对不同时间尺度下的可塑性响应是否共享相似的潜在分子机制仍知之甚少，而这一问题对于评估可塑性对演化轨迹的影响至关重要。为解决这一研究空白，本研究对三刺鱼（Gasterosteus aculeatus）成体肌肉转录组（muscle transcriptome）中响应发育温度的差异基因表达进行了分析：实验对象先在12℃、18℃或24℃环境中培育至孵化，随后在18℃条件下饲养9个月。同时，本研究将该结果与另一组实验的差异基因表达数据进行对比：该组三刺鱼在18℃环境下发育至成体，随后作为成体分别在5℃和25℃下进行热驯化（thermal acclimation），分析其响应成体热驯化的基因表达变化。成体热驯化分别在冷驯化与热驯化条件下，影响了7940和7015个基因的表达，其中4851个基因在两种处理中均出现表达响应。与之形成鲜明对比的是，仅33个和29个基因分别受低温发育与高温发育的调控。绝大多数受发育温度调控的基因，同时也会受到成体驯化温度的影响。大量在成体热驯化过程中差异表达的基因，与此前已报道的温度依赖性DNA甲基化（DNA methylation）模式变化存在关联，这提示表观遗传机制（epigenetic mechanisms）在驯化过程中调控基因表达可塑性的过程中发挥了重要作用。综上，本研究结果表明，发育可塑性对基因表达的持续影响与成体热驯化的基因表达效应存在显著相似性，凸显了不同生命阶段的可塑性响应之间存在潜在的机制关联。