Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage.
Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage.
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DOI：
10.1186/s13059-022-02834-4
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发表时间：
2022-12-19
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
作者：
大白菜（Brassica rapa ssp.）pekinensis）经历了全基因组三倍体事件，因此具有三个亚基因组：最少部分、中等部分和最多部分的亚基因组。环境变化影响叶片发育，进而影响产量。为了提高产量和对不同气候情景的抗性，需要全面了解叶片发育，包括深入了解细胞类型的全部多样性及其特异性的转录网络。在这里，我们通过对30，000个单个细胞进行单细胞RNA测序，以单细胞分辨率生成大白菜叶片的转录景观。我们表征7个主要的细胞类型与19个转录不同的细胞簇的基础上报告的标记基因的表达。我们发现，在最少的分馏亚基因组中的基因主要表达相比，在介质和最分馏的亚基因组在不同的细胞类型。此外，我们产生了单细胞转录图谱的叶片响应高温。我们发现，热应激不仅影响基因表达的细胞类型特异性的方式，但也影响亚基因组的优势。我们的研究突出了不同细胞类型中的转录网络，并提供了更好的理解在叶片发育过程中的转录调控和热胁迫下的转录响应。在线版本包含补充材料，可通过10.1186/s13059-022-02834-4获得。
Chinese cabbage (Brassica rapa ssp. pekinensis) experienced a whole-genome triplication event and thus has three subgenomes: least fractioned, medium fractioned, and most fractioned subgenome. Environmental changes affect leaf development, which in turn influence the yield. To improve the yield and resistance to different climate scenarios, a comprehensive understanding of leaf development is required including insights into the full diversity of cell types and transcriptional networks underlying their specificity. Here, we generate the transcriptional landscape of Chinese cabbage leaf at single-cell resolution by performing single-cell RNA sequencing of 30,000 individual cells. We characterize seven major cell types with 19 transcriptionally distinct cell clusters based on the expression of the reported marker genes. We find that genes in the least fractioned subgenome are predominantly expressed compared with those in the medium and most fractioned subgenomes in different cell types. Moreover, we generate a single-cell transcriptional map of leaves in response to high temperature. We find that heat stress not only affects gene expression in a cell type-specific manner but also impacts subgenome dominance. Our study highlights the transcriptional networks in different cell types and provides a better understanding of transcriptional regulation during leaf development and transcriptional response to heat stress in Chinese cabbage. The online version contains supplementary material available at 10.1186/s13059-022-02834-4.
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DOI：
10.1109/tvcg.2014.2346248
发表时间：
2014-12
影响因子：
5.2
作者：
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影响因子：
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影响因子：
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