Data from: The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region

Developmental responses to nutritional variation represent one of the ecologically most important classes of adaptive plasticity. However, knowledge of genome-wide patterns of nutrition-responsive gene expression is limited. Here, we studied genome-wide transcriptional responses to nutritional variation and their dependency on trait and sex in the beetle Onthophagus taurus. We find that averaged across the transcriptome, nutrition contributes less to overall variation in gene expression than do sex or body region, but that for a modest subset of genes nutrition is by far the most important determinant of expression variation. Furthermore, our results reject the hypothesis that a common machinery may underlie nutrition-sensitive development across body regions. Instead, we find that magnitude (measured by number of differentially expressed contigs), composition (measured by functional enrichment) and evolutionary consequences (measured by patterns of sequence variation) are heavily dependent on exactly which body region is considered and the degree of sexual dimorphism observed on a morphological level. More generally, our findings illustrate that studies into the developmental mechanisms and evolutionary consequences of nutrition-biased gene expression must take into account the dynamics and complexities imposed by other sources of variation in gene expression such as sexual dimorphism and trait type.生物体对营养变化的发育响应，是适应性可塑性（adaptive plasticity）这一生态学领域中最为重要的类别之一。然而，目前学界关于全基因组（genome-wide）范围内营养响应性基因表达模式的认知仍较为有限。本研究以金牛嗡蜣螂（Onthophagus taurus）为实验材料，探究了其对营养变化的全基因组转录响应，以及该响应与性状和性别的依赖关系。 研究结果显示，从整个转录组（transcriptome）的平均水平来看，相较于性别或身体区域，营养对基因表达整体变异的贡献度更低；但对于少量基因子集而言，营养无疑是其表达变异最关键的决定因素。此外，本研究结果否定了“不同身体区域的营养敏感性发育共享一套核心调控机制”这一假说。 与之相反，我们发现：响应幅度（以差异表达重叠群（differentially expressed contigs）的数量衡量）、组成（以功能富集分析（functional enrichment）结果衡量）以及进化后果（以序列变异（sequence variation）模式衡量），均严格依赖于所研究的具体身体区域，以及形态学层面观测到的性二态性（sexual dimorphism）程度。 总体而言，本研究结果表明，针对营养偏向性基因表达（nutrition-biased gene expression）的发育机制与进化后果开展的研究，必须充分考虑基因表达其他变异来源（如性二态性与性状类型）所带来的动态性与复杂性。