Heinrich-Heine-University, Institute for Cell Biology and Zoology, Universitätsstrasse 1, 40225, Düsseldorf, Germany.
Fraunhofer IME, Institute for Molecular Ecology, Am Aberg 1, 57392, Schmallenberg, Germany.
BMC Genomics. 2019 Nov 21;20(1):894. doi: 10.1186/s12864-019-6268-y.
Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton's content of the essential polyunsaturated omega-3 fatty acid eicosapentaenoic acid (EPA) has been repeatedly shown to limit secondary production in the major zooplankton herbivore genus Daphnia. Despite extensive research efforts on the biological model organism Daphnia, and the availability of several Daphnia genomes, little is known regarding the molecular mechanisms underlying the limitations in Daphnia related to dietary EPA availability.
We used RNA-seq to analyse the transcriptomic response of Daphnia magna which were fed with two different diets - each with or without supplementation of EPA - at two different temperature levels (15 and 20 °C). The transcripts were mapped to the D. magna genome assembly version 2.4, containing 26,646 translations. When D. magna fed on green alga, changing the temperature provoked a differential expression of 2001 transcripts, and in cyanobacteria-fed daphnia, 3385 transcripts were affected. The supplementation of EPA affected 1635 (on the green algal diet), or 175 transcripts (on the cyanobacterial diet), respectively. Combined effects for diet and temperature were also observed (669 for the green algal and 128 transcripts for the cyanobacterial diet). Searching for orthologous genes (COG-analysis) yielded a functional overview of the altered transcriptomes. Cross-matched transcript sets from both feed types were compiled to illuminate core responses to the factors temperature and EPA-supplementation.
Our highly controlled eco-physiological experiments revealed an orchestrated response of genes involved in the transformation and signalling of essential fatty acids, including eicosanoid-signalling pathways with potential immune functions. We provide an overview of downstream-regulated genes, which contribute to enhance growth and reproductive output. We also identified numerous EPA-responsive candidate genes of yet unknown function, which constitute new targets for future studies on the molecular basis of EPA-dependent effects at the freshwater plant-herbivore interface.
浮游植物的营养质量是淡水食物网中植物-食草动物界面营养传递效率的主要决定因素。特别是，浮游植物中必需的多不饱和ω-3 脂肪酸二十碳五烯酸（EPA）的含量已被反复证明限制了主要浮游动物属 Daphnia 的次级生产力。尽管对生物模式生物 Daphnia 进行了广泛的研究，并提供了几个 Daphnia 基因组，但对于与 EPA 可利用性相关的 Daphnia 限制的分子机制知之甚少。
我们使用 RNA-seq 分析了 Daphnia magna 的转录组响应，这些 Daphnia magna 分别用两种不同的饮食 - 每种饮食都含有或不含有 EPA 补充剂 - 在两种不同的温度水平（15 和 20°C）下喂养。这些转录本被映射到 D. magna 基因组组装版本 2.4，包含 26646 个翻译。当 D. magna 以绿藻为食时，改变温度会引起 2001 个转录本的差异表达，而在以蓝藻为食的 Daphnia 中，有 3385 个转录本受到影响。EPA 的补充分别影响了绿藻饮食中的 1635 个（或蓝藻饮食中的 175 个）转录本。饮食和温度的综合影响也观察到（绿藻饮食中有 669 个，蓝藻饮食中有 128 个）。搜索同源基因（COG 分析）提供了改变的转录组的功能概述。从两种饲料类型交叉匹配的转录组被编译，以阐明对温度和 EPA 补充因素的核心响应。
我们的高度受控生态生理学实验揭示了参与必需脂肪酸转化和信号转导的基因的协调反应，包括具有潜在免疫功能的类二十烷酸信号通路。我们提供了一个下游调节基因的概述，这些基因有助于提高生长和生殖产量。我们还鉴定了许多 EPA 反应候选基因，其功能未知，它们构成了未来研究淡水植物-食草动物界面上 EPA 依赖性影响的分子基础的新目标。
