Asselman Jana, Pfrender Michael E, Lopez Jacqueline A, De Coninck Dieter I M, Janssen Colin R, Shaw Joseph R, De Schamphelaere Karel A C
Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab unit, Ghent University, J. Plateaustraat 22, 9000, Gent, Belgium; Department of Biological Sciences, University of Notre Dame, Notre Dame, 46556, IN, USA.
Mol Ecol. 2015 Apr;24(8):1844-55. doi: 10.1111/mec.13148. Epub 2015 Apr 2.
Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.
尽管基因组数据大幅增加，但我们对基因功能及其对环境刺激的转录反应的了解仍然有限。在此，我们使用模式关键物种大型溞，在基因家族历史背景下研究基因的环境反应，以更好地理解基因组结构与基因功能在应对环境刺激时的关系。大型溞接受了五种不同处理，每种处理包括添加五种蓝藻物种之一的饮食，以及仅以绿藻为食的对照处理。暴露于这五种蓝藻物种中的每一种的大型溞的差异基因表达谱表明，具有已知功能的基因更有可能被不同的表达谱共享，而大型溞谱系特有的基因更有可能在给定的表达谱中是独特的。此外，虽然跨处理类型仅少数非谱系特异性基因是保守的，但在功能水平上表达谱存在高度重叠。不同蓝藻处理之间功能反应的保守性可归因于同一基因家族内不同旁系同源基因的处理特异性表达。与文献中可用的基因表达数据比较表明，与绿藻饮食相比，含蓝藻物种的饮食中的营养成分差异是蓝藻对大型溞产生影响的主要驱动因素。我们得出结论，大型溞在不同蓝藻处理之间保守的功能反应是通过旁系同源基因家族的交替调控介导的。
