Journal of Genetics and Genomics
Abstract
As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses, and characterize transcriptomes for a total of 237,431 individual cells. We identify fifteen and nine cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell-type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.
| 论文编号: | DOI:10.1016/j.jgg.2021.06.001 |
| 论文题目: | Single-Cell Transcriptome Atlas of the Leaf and Root of Rice Seedlings |
| 英文论文题目: | Single-Cell Transcriptome Atlas of the Leaf and Root of Rice Seedlings |
| 第一作者: | Yu Wang, Qing Huan, Ke Li, Wenfeng Qian |
| 英文第一作者: | Yu Wang, Qing Huan, Ke Li, Wenfeng Qian |
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| 发表年度: | 2021-06-22 |
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| 摘要: | As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses, and characterize transcriptomes for a total of 237,431 individual cells. We identify fifteen and nine cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell-type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology. |
| 英文摘要: | As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses, and characterize transcriptomes for a total of 237,431 individual cells. We identify fifteen and nine cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell-type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology. |
| 刊物名称: | Journal of Genetics and Genomics |
| 英文刊物名称: | Journal of Genetics and Genomics |
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| 其它备注: | Yu Wang, Qing Huan, Ke Li, Wenfeng Qian. Single-Cell Transcriptome Atlas of the Leaf and Root of Rice Seedlings. Journal of Genetics and Genomics. DOI:10.1016/j.jgg.2021.06.001 |
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