A cell atlas of temperature-dependent gene activities in the flower

植物暴露在一个与生俱来的环境中，这取决于当地的栖息地。因此，植物进化出了复杂的适应机制，不同的器官和细胞类型的环境反应程序也不同。一个很好的例子是花发育的环境稳定性，这是决定植物栖息地范围的关键因素。一旦决定开花，无论当地环境如何，花器官的发育都需要得到强有力的维持。然而，不同细胞类型和单个细胞中的基因活性如何受到温度等环境因素的控制在很大程度上仍是未知的。新的单细胞组学技术已经开始揭示多细胞生物体内在的细胞异质性。然而，植物细胞对单细胞组学提出了特殊的挑战，因为细胞壁的存在加剧了单细胞的分离。我们已经在植物中建立了单核RNA-seq，这使得我们能够在细胞核中‘冻结’天然的转录状态，从而克服了通常使用的导致许多逆境相关基因激活的原生质体技术的局限性。因此，这种方法使我们能够研究转录活动中的环境反应。这个项目的目的是使用我们的SnRNA-seq方法来生成与花的温度适应相关的转录变化的细胞图谱。其目标是在三个物种中产生依赖温度的细胞型基因活性图谱：模式植物拟南芥、其近亲豆蔻草和作物植物茄子番茄。此外，我们利用拟南芥丰富的自然变异知识，通过询问不同的生态型来反映该物种在大的全球栖息地范围内对不同局部环境的适应。通过结合关于细胞类型特异性基因活动差异的信息和关于自然遗传变异的信息，我们可以识别参与调节花发育的温度稳定性的候选基因。该项目将为使用单细胞组学技术了解植物环境反应的细胞类型特异性提供创新的概念验证，使这些方法在未来应用于其他环境条件和生物学问题。

Plants are exposed to an environment that is inherently heterogeneous depending on the local habitat. Therefore, plants have evolved intricate adaptive mechanisms, and different organs and cell types vary in their environmental response programs. An excellent example for this is the environmental robustness of flower development, which is a key factor in determining the habitat range of plants. Once the decision to bloom has been made, floral organ development need to be robustly maintained irrespective of the local environment. However, it is still largely unknown how gene activity in different cell types and individual cells is controlled by environmental factors such as temperature.Novel single-cell omics technologies have started to unravel the intrinsic cellular heterogeneity in multicellular organisms. However, plant cells pose specific challenges to single cell omics, because the isolation of single cells is aggravated by the presence of a cell wall. We have established single nucleus RNA-seq in plants, which allows us to ‘freeze’ the native transcript states in nuclei and thereby overcomes the limitation of commonly used protoplasting techniques that result in the activation of many stress-related genes. Thus, this method allows us to study environmental responses in transcriptional activity. This project aims at using our snRNA-seq method to generate a cellular atlas of transcriptional changes associated with temperature adaptation in the flower. The goal is to generate temperature-dependent cell type atlases of gene activity in three species: the model plant Arabidopsis thaliana, its close relative Cardamine hirsuta and the crop plant species Solanum lycopersicum. In addition, we make use of the rich knowledge of natural variation within Arabidopsis by interrogating different ecotypes that reflect adaptations to different local environments within the large global habitat range of this species. By combining information on cell-type specific differences in gene activities with information on natural genetic variation, we can identify candidate genes involved in mediating temperature robustness of flower development. This project will provide an innovative proof-of-concept for using single cell omics technologies to understand cell-type specificity of environmental responses in plants, allowing these methods to be applied to other environmental conditions and biological questions in the future.