Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin

Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three years of common conditions, we find highly correlated expression patterns (Pearson’s r = 0.992) among most genes. However, sixty-six genes were differentially expressed, including many ribosomal protein and biomineralization genes, all of which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, “bone” development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine re-growth experiment revealed that urchins of southern origin re-grew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high dispersal-mediated gene flow in this marine species.

在异质性景观中，不同种群的基因调控可能存在适应性差异，以此调整生理机能以适配当地生境。这类差异可能源于驯化作用，或是不同生境间的遗传固定变异。本研究采用同质园实验（common garden experiment），对跨度达1700公里、平均水温差5℃至8℃的紫球海胆（Strongylocentrotus purpuratus）不同种群间的基因表达差异进行评估。在统一培养条件下饲养三年后，对18883个基因的表达谱进行分析，我们发现绝大多数基因的表达模式具有高度相关性（皮尔逊相关系数（Pearson’s r）为0.992）。然而，有66个基因呈现差异表达，其中包含大量核糖体蛋白（ribosomal protein）与生物矿化（biomineralization）相关基因，所有这些基因在源自南部种群的海胆中均呈现更高的表达水平。基因功能分析显示，与核糖体功能、代谢、物质转运、“骨骼”发育以及应激响应相关的基因，均存在细微但普遍的表达差异。与基因表达模式相符的是，一项事后棘再生实验结果表明，源自南部种群的海胆棘再生速率高于北部种群海胆。上述结果表明，不同生境间的基因调控可能存在受遗传控制的、具有潜在适应性的差异；同时，基因表达差异所承受的选择压力足够强，足以克服该海洋物种因高扩散能力介导的基因流。