Each plant cell is characterized by its specific function, developmental stage, and interaction with its environment. Understanding the differential use of the genome by each cell/cell type composing the plant and its regulation in response to environmental changes provides a new understanding of gene function, regulation, and networks. In this presentation, focusing on the symbiotic interaction between soybean plants and Bradyrhizobium diazoefficiens, nitrogen-fixing symbiotic bacteria, we will present the use of single-cell omics and high-resolution spatial transcriptomics to 1) reveal the cellular complexity of the infection zone of the soybean nodule, 2) expose the role of the sub-cellular compartmentalization of plant transcripts as a regulatory mechanism of protein translation, and 3) support the functional characterization of new genes controlling this symbiosis. For instance, we will present the role of the nanodomain-associated protein GmFWL3 in controlling the infection of the soybean cells of the nodule by B. diazoefficiens. We will also present our data in the context of Tabula Glycine, a single-cell resolution transcriptome atlas of the soybean plant. For instance, the mining of Tabula Glycine supports the selection of meaningful transcription factor genes that likely cooperate to drive cell-type-specific transcriptomic programs in the B. diazoefficiens-infected soybean cells of the nodule.