24-hour age difference causes twice as much gene expression divergence as 100 generations of adaptation to a novel environment

Gene expression profiling is one of the most reliable high-throughput phenotyping methods, allowing to quantify the transcript abundance of expressed genes. Because many biotic and abiotic factors influence gene expression, it is recommended to control them as tightly as possible. Here we show that the 24-hour age difference of Drosophila simulans females that were subjected to RNA-Seq five and six days after eclosure results in more than 2000 differentially expressed genes. This is twice the number of genes that changed gene expression during 100 generations of evolution in a novel hot laboratory environment. Importantly, most of the genes differing in expression due to age introduce false positives/negatives if an adaptive gene expression analysis is not controlled for age. Our results indicate that tightly controlled experimental conditions, including precise developmental staging, are needed for reliable gene expression analyses, in particular in an evolutionary framework.

基因表达谱分析（Gene expression profiling）是目前最可靠的高通量表型分析（high-throughput phenotyping）方法之一，可对已表达基因的转录本丰度（transcript abundance）进行定量检测。由于诸多生物与非生物因子均可影响基因表达，因此需尽可能严格地控制这些影响因素。本研究发现，对羽化后第5天和第6天的拟果蝇（Drosophila simulans）雌性个体进行RNA测序（RNA-Seq）时，仅24小时的年龄差异即可使超过2000个基因出现差异表达。该数值是在新型高温实验室环境中历经100代进化后基因表达发生改变的基因数的两倍。尤为重要的是，若在适应性基因表达分析中未对年龄因素加以控制，多数因年龄差异出现表达量差异的基因都会造成假阳性/假阴性结果。本研究结果表明，要开展可靠的基因表达分析，尤其是在进化研究框架下，必须采用严格控制的实验条件，其中包括精确的发育阶段分期。