Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis. The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed. Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.

中文翻译：

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橡树对不同的菌根真菌表现出常见的局部但特定的远距离基因调控反应。


树根与多种共生菌根真菌的关联对整个植物的功能具有独特的影响。未经检验的解释可能是，这种效应变异性与不同真菌对局部和远处植物器官基因表达的不同影响有关。使用大规模转录组测序方法，我们比较了三种外生菌根真菌 (EMF) 和一种兰花菌根真菌 (OMF) 对定植根（局部）、非定植根（短距离）和叶子（长距离）基因调控的影响参考最近发表的橡树基因组，对夏栎克隆 DF159 进行了克隆。由于不同的菌根真菌在不同的时间跨度和不同程度的共生结构发育中形成共生，我们对接种但非菌根的植物进行了采样，但已报道了其显着的共生效应。通过真菌转录本分析评估真菌的局部根定殖。在分析的关联阶段，EMF 对植物发育产生显着的物种特异性影响，但 OMF 却没有。在局部水平上，确定了一组常见的植物差异表达基因（DEG），其对三种 EMF 的响应模式相似，但对 OMF 则不然。这些核心 DEG 中的大多数都被下调，并且对应于已经描述的以及与建立 EMF 共生相关的新功能。对高度定植根中两种 EMF 的真菌转录物的分析也揭示了共生建立的开始。相比之下，在 OMF 中，DEG 主要与植物防御相关。 在短距离处，四种真菌的转录组反应具有高度特异性，而在长距离处，这种反应在叶子中进一步增强，在处理之间几乎没有发现共同的 DEG。值得注意的是，没有观察到 EMF 的系统发育与基因表达模式之间的相关性。使用克隆橡树使我们能够识别出三种不同 EMF 定殖的根中的核心转录程序，支持共同 EMF 共生途径的存在。相反，非定植器官中的特定反应与不同 EMF 对植物性能的特定影响更密切相关。