Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics

Keyi Ye (), Fengjiao Bu, Liyuan Zhong, Zhaonian Dong, Zhaoxu Ma, Zhanpeng Tang, Yu Zhang, Xueyong Yang, Xun Xu, Ertao Wang, William J. Lucas, Sanwen Huang, Huan Liu () and Jianshu Zheng ()
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Keyi Ye: Chinese Academy of Agricultural Sciences
Fengjiao Bu: Chinese Academy of Agricultural Sciences
Liyuan Zhong: BGI Research
Zhaonian Dong: Chinese Academy of Agricultural Sciences
Zhaoxu Ma: Chinese Academy of Agricultural Sciences
Zhanpeng Tang: Chinese Academy of Agricultural Sciences
Yu Zhang: Chinese Academy of Agricultural Sciences
Xueyong Yang: Chinese Academy of Agricultural Sciences
Xun Xu: BGI Research
Ertao Wang: Chinese Academy of Sciences
William J. Lucas: Chinese Academy of Agricultural Sciences
Sanwen Huang: Chinese Academy of Agricultural Sciences
Huan Liu: BGI Research
Jianshu Zheng: Chinese Academy of Agricultural Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Legumes acquire nitrogen-fixing ability by forming root nodules. Transferring this capability to more crops could reduce our reliance on nitrogen fertilizers, thereby decreasing environmental pollution and agricultural production costs. Nodule organogenesis is complex, and a comprehensive transcriptomic atlas is crucial for understanding the underlying molecular events. Here, we utilized spatial transcriptomics to investigate the development of nodules in the model legume, Lotus japonicus. Our investigation has identified the developmental trajectories of two critical regions within the nodule: the infection zone and peripheral tissues. We reveal the underlying biological processes and provide gene sets to achieve symbiosis and material exchange, two essential aspects of nodulation. Among the candidate regulatory genes, we illustrate that LjNLP3, a transcription factor belonging to the NIN-LIKE PROTEIN family, orchestrates the transition of nodules from the differentiation to maturation. In summary, our research advances our understanding of nodule organogenesis and provides valuable data for developing symbiotic nitrogen-fixing crops.

Date: 2024
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DOI: 10.1038/s41467-024-50737-8

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