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.

营养变异引发的发育响应，是生态学领域最为重要的适应性可塑性（adaptive plasticity）类别之一。然而，当前学界对营养响应基因表达的全基因组模式认知仍较为有限。本研究以嗡蜣螂（Onthophagus taurus）为对象，探究其营养变异诱导的全基因组转录响应，以及该响应对性状与性别的依赖性。我们发现，在转录组（transcriptome）整体水平平均而言，营养对基因表达总变异的贡献度低于性别或躯体区域；但在少量基因子集当中，营养是其表达变异最关键的决定因素。此外，本研究结果不支持“不同躯体区域的营养敏感发育共享统一调控机制”这一假说。与之相反，我们发现：转录响应的规模（以差异表达重叠群（contigs）的数量衡量）、组成（以功能富集分析（functional enrichment）结果衡量）以及进化效应（以序列变异模式衡量），均高度依赖于所关注的具体躯体区域，以及形态层面观测到的性二态性（sexual dimorphism）程度。更具普遍意义的是，本研究结果表明，针对营养偏向性基因表达（nutrition-biased gene expression）的发育机制与进化效应开展的研究，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。