Spatially resolved transcriptomics reveals plant host responses to pathogens
Spatially resolved transcriptomics reveals plant host responses to pathogens
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DOI：
10.1186/s13007-019-0498-5
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发表时间：
2019-10-10
期刊：
影响因子：
5.1
通讯作者：
Clark, Matthew D.
中科院分区：
文献类型：
--
作者：
Giolai, Michael;Verweij, Walter;Clark, Matthew D.
背景：对复杂模型系统的彻底理解需要对生物体不同细胞类型的过程进行表征。这可以通过大规模的高通量空间转录组学来实现。然而，对于植物模型系统，这仍然具有挑战性，因为合适的转录组学方法很少可用。在这里，我们提出了GaST-seq（网格辅助空间转录组测序），这是一种易于采用的微尺度空间转录组工作流程，可以研究植物组织小区域的表达谱，成本仅为现有基于测序的方法的一小部分。结果：我们将gaas -seq方法与广泛使用的文库制备方法（Illumina TruSeq）进行了比较。在空间实验中，我们表明GaST-seq方法足够敏感，可以识别植物器官之间的表达差异。我们进一步评估了暴露于细菌分子鞭毛蛋白22的拟南芥叶片的空间转录组反应，并表明真核感染（白垩白杆菌）获得了宿主和病原体的空间转录组。结论：我们的方法可以用于鉴定已知的、快速的鞭毛蛋白22诱导基因、植物对细菌攻击的免疫反应途径以及这些途径相关基因的空间表达模式。
Background: Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present GaST-seq (Grid-assisted, Spatial Transcriptome sequencing), an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.Results: We compare the GaST-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the GaST-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22, and show that with eukaryotic (Albugo laibachii) infection both host and pathogen spatial transcriptomes are obtained.Conclusion: We show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.