Data from: Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

AbstractSpecies respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we use de novo transcriptome assembly and RNA-seq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6,413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million years of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved vs. diverged patterns of expression. We conclude that natural selection has likely played a role in shaping plastic responses to environment in these species., Usage notesdata for: Conservation and divergence of gene expression plasticity following ~140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca and Picea engelmannii)This archive includes raw data and scripts used for the paper. .dat files contain annotation information in blast2go format.lodgepole_pine_interior_spruce_RNAseq_archive.tar.gz

摘要：物种通过遗传适应与表型可塑性的协同作用应对环境胁迫，二者在气候变化背景下均对物种存活至关重要。通过解析可塑性响应的分子基础并比较不同物种间的响应模式，可揭示此类性状的演化机制。本研究采用从头转录组组装（de novo transcriptome assembly）与RNA测序（RNA-seq）技术，探究扭叶松（Pinus contorta）与内陆云杉（白云杉（Picea glauca）和恩格尔曼云杉（Picea engelmannii）的天然杂交种群）在温度、湿度及光照条件处理下的基因表达模式差异。本研究发现，两个物种的基因表达均广泛受到处理条件的调控：云杉与扭叶松中分别鉴定出6413个和11658个差异表达基因（differentially expressed genes）。通过比较两个物种的表达模式，我们发现尽管二者已有1.4亿年的演化分歧，但所有具有差异表达的直系同源基因（orthologs）中，有74%的表达模式在两个物种中均保守。此外我们还发现，驱动表达模式的具体处理条件，在表达模式保守与分化的基因之间存在差异。综上，我们认为自然选择可能在塑造这两个物种的环境可塑性响应过程中发挥了重要作用。
使用说明：本数据关联研究聚焦于扭叶松（Pinus contorta）与内陆云杉（白云杉Picea glauca和恩格尔曼云杉Picea engelmannii）经约1.4亿年演化后的基因表达可塑性保守性与分化。本归档文件包含本论文所用的原始数据与分析脚本。其中.dat格式文件包含BLAST2GO（blast2go）格式的注释信息。归档文件名为lodgepole_pine_interior_spruce_RNAseq_archive.tar.gz