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Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves

View ORCID ProfileKeke Xia, Hai-Xi Sun, Jie Li, Jiming Li, Yu Zhao, Ruiying Chen, Guangyu Liu, Zhiyong Chen, Ruilian Yin, View ORCID ProfileShijie Hao, Jing Wang, Qing Xie, Jiangshan Xu, Yuxiang Li, Ao Chen, Longqi Liu, Ye Yin, Huanming Yang, Jian Wang, View ORCID ProfileYing Gu, Xun Xu
doi: https://doi.org/10.1101/2021.10.20.465066
Keke Xia
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Hai-Xi Sun
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Jie Li
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
2College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049 China
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Jiming Li
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Yu Zhao
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Ruiying Chen
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
3College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Guangyu Liu
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Zhiyong Chen
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Ruilian Yin
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
2College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049 China
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Shijie Hao
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
2College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049 China
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Jing Wang
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Qing Xie
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Jiangshan Xu
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
2College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049 China
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Yuxiang Li
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Ao Chen
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Longqi Liu
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
4Shenzhen Key Laboratory of Single Cell Omics, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
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Ye Yin
5BGI Genomics, BGI-Shenzhen, Shenzhen 518083, Guangdong, China
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Huanming Yang
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
6James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China.
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Jian Wang
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
6James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China.
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  • For correspondence: xuxun@genomics.cn guying@genomics.cn wangjian@genomics.cn
Ying Gu
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
7Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
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  • For correspondence: xuxun@genomics.cn guying@genomics.cn wangjian@genomics.cn
Xun Xu
1BGI-Shenzhen, Shenzhen 518083, Guangdong, China
7Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
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  • For correspondence: xuxun@genomics.cn guying@genomics.cn wangjian@genomics.cn
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Summary

Understanding the complex functions of plant leaves requires spatially resolved gene expression profiling with single-cell resolution. However, although in situ gene expression profiling technologies have been developed, this goal has not yet been achieved. Here, we present the first in situ single-cell transcriptome profiling in plant, scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing), which enabled the bona fide single-cell spatial transcriptome of Arabidopsis leaves. We successfully characterized subtle but significant transcriptomic differences between upper and lower epidermal cells. Furthermore, with high-resolution location information, we discovered the cell type-specific spatial gene expression gradients from main vein to leaf edge. By reconstructing those spatial gradients, we show for the first time the distinct spatial developmental trajectories of vascular cells and guard cells. Our findings show the importance of incorporating spatial information for answering complex biological questions in plant, and scStereo-seq offers a powerful single cell spatially resolved transcriptomic strategy for plant biology.

Competing Interest Statement

The authors declare the following competing interests: The chip, procedure and applications of Stereo-seq are covered in pending patents. Employees of BGI have stock holdings in BGI.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 21, 2021.
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Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves
Keke Xia, Hai-Xi Sun, Jie Li, Jiming Li, Yu Zhao, Ruiying Chen, Guangyu Liu, Zhiyong Chen, Ruilian Yin, Shijie Hao, Jing Wang, Qing Xie, Jiangshan Xu, Yuxiang Li, Ao Chen, Longqi Liu, Ye Yin, Huanming Yang, Jian Wang, Ying Gu, Xun Xu
bioRxiv 2021.10.20.465066; doi: https://doi.org/10.1101/2021.10.20.465066
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Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves
Keke Xia, Hai-Xi Sun, Jie Li, Jiming Li, Yu Zhao, Ruiying Chen, Guangyu Liu, Zhiyong Chen, Ruilian Yin, Shijie Hao, Jing Wang, Qing Xie, Jiangshan Xu, Yuxiang Li, Ao Chen, Longqi Liu, Ye Yin, Huanming Yang, Jian Wang, Ying Gu, Xun Xu
bioRxiv 2021.10.20.465066; doi: https://doi.org/10.1101/2021.10.20.465066

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