Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology
Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology
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DOI：
10.1016/j.plantsci.2022.111486
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发表时间：
2022-10-06
期刊：
影响因子：
5.2
通讯作者：
Libault, Marc
中科院分区：
文献类型：
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作者：
Alan Cervantes-Perez, Sergio;Thibivillliers, Sandra;Libault, Marc
植物单细胞RNA-seq技术以单细胞分辨率量化植物转录本的丰度。破译每个植物细胞的转录组，它们在植物细胞发育过程中的调控，以及它们对环境胁迫的反应将支持基因的功能研究，建立精确的转录程序，预测更准确的基因调控网络，以及从长远来看，设计从头基因途径来增强选定的作物性状。在这篇综述中，我们将讨论与植物单细胞转录组的生成和分析相关的机遇，挑战和问题，并分享尝试性的解决方案。我们将讨论使用植物原生质体与细胞核在各种植物物种和器官上进行单细胞RNA-seq实验的好处和局限性，基于转录组学特征的植物细胞类型的功能注释，细胞发育期间或响应环境胁迫的植物基因动态调控的表征，需要表征和整合额外的组学数据集层，以在单细胞水平上捕获新的分子模式并揭示其因果关系，沉积和访问单细胞数据集，以及植物科学家对该技术的可访问性。
Plant single-cell RNA-seq technology quantifies the abundance of plant transcripts at a single-cell resolution. Deciphering the transcriptomes of each plant cell, their regulation during plant cell development, and their response to environmental stresses will support the functional study of genes, the establishment of precise transcriptional programs, the prediction of more accurate gene regulatory networks, and, in the long term, the design of de novo gene pathways to enhance selected crop traits. In this review, we will discuss the opportunities, challenges, and problems, and share tentative solutions associated with the generation and analysis of plant single-cell transcriptomes. We will discuss the benefit and limitations of using plant protoplasts vs. nuclei to conduct single-cell RNA-seq experiments on various plant species and organs, the functional annotation of plant cell types based on their transcriptomic profile, the characterization of the dynamic regulation of the plant genes during cell development or in response to environmental stress, the need to characterize and integrate additional layers of -omics datasets to capture new molecular modalities at the single-cell level and reveal their causalities, the deposition and access to single-cell datasets, and the accessibility of this technology to plant scientists.