Single‐cell RNA‐seq of Lotus japonicus provide insights into identification and function of root cell types of legume

doi:10.1111/jipb.13435

J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (5): 1147-1152.DOI: 10.1111/jipb.13435

• Functional Omics and Systems Biology • Previous Articles Next Articles

Single‐cell RNA‐seq of Lotus japonicus provide insights into identification and function of root cell types of legume

Zhanmin Sun^1†, Sanjie Jiang^2†, Dan Wang^3†, Linxia Li¹, Boxin Liu², Qifan Ran⁴, Lizhen Hu⁵, Junbo Xiong⁶, Yixiong Tang¹, Xiaofeng Gu¹, Yanmin Wu^1* and Zhe Liang^1*

1. Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
2. BGI Genomics, Shenzhen 518083, China;
3. Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Nanchong 637002, China;
4. Chongqing Academy of Animal Sciences, Chongqing 402460, China;
5. Institute of Animal and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China;
6. Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan 430072, China
^†Zhanmin Sun, Sanjie Jiang, and Dan Wang contributed equally to this work.
^*Correspondences: Yanmin Wu (wuyanmin@caas.cn); Zhe Liang (liangzhe@caas.cn, Dr. Liang is fully responsible for the distribution of the materials associated with this article)

Received:2022-10-03 Accepted:2022-12-16 Online:2023-01-31 Published:2023-05-01

Abstract

Abstract: The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single‐cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume. We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single‐cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes.

Key words: genome, legume, Lotus japonicus, single‐cell RNA‐seq

Zhanmin Sun, Sanjie Jiang, Dan Wang, Linxia Li, Boxin Liu, Qifan Ran, Lizhen Hu, Junbo Xiong, Yixiong Tang, Xiaofeng Gu, Yanmin Wu and Zhe Liang. Single‐cell RNA‐seq of Lotus japonicus provide insights into identification and function of root cell types of legume[J]. J Integr Plant Biol., 2023, 65(5): 1147-1152.

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Single‐cell RNA‐seq of Lotus japonicus provide insights into identification and function of root cell types of legume

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