Spatially resolved transcriptomic analysis of the germinating barley grain.
Spatially resolved transcriptomic analysis of the germinating barley grain.
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DOI：
10.1093/nar/gkad521
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发表时间：
2023-08-25
影响因子：
14.9
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中科院分区：
文献类型：
--
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种子是人类重要的卡路里来源，也是开花植物生命周期中的一个独特阶段。在种子萌发过程中，胚经历主要的发育转变成为幼苗。由于缺乏空间信息或现有方法的低通量，研究单个种子细胞类型中的基因表达一直具有挑战性。为了克服这些限制，开发了用于发芽大麦谷粒的空间转录组学工作流程。这种方法能够高通量分析空间基因表达，揭示特定的空间表达模式的各种功能基因类别在亚组织水平。这项研究揭示了超过14000个基因差异调节在第一个24小时后吸胀。单个基因，如水通道蛋白基因家族，淀粉降解，细胞壁修饰，运输过程，核糖体蛋白和转录因子，被发现具有特定的空间表达模式随着时间的推移。使用空间自相关算法，我们确定了生长素运输基因，随着时间的推移，越来越集中表达的子领域内的胚胎，这表明他们在建立胚胎轴的作用。总的来说，我们的研究提供了一个前所未有的空间分辨大麦发芽细胞图谱，并确定了特定的功能基因组学目标，以更好地了解发芽过程中的细胞限制性过程。数据可在https://spatial.latrobe.edu.au/上查看。
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
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