Disclosing Revealing the temporal and spatial expression of each gene is predominantly importantcritical for the understanding of plant organ development. To this end, There is increasing demand for the construction of an integrated transcriptomic atlases using different multiple types of transcriptome data as a means of achieving this aim is increasingly demanded. in increasing demand. In this study, we sequencesequenced 315 soybean tissues during over the course of the full whole developmental cycle by bulk RNA-seq and sequencesequenced 5 representative organs (root, noduleroots, nodules, shoot apical meristem, leaf and stemmeristems, leaves and stems) by snRNA-seq and Stereo-seq, respectively. Integrating these transcriptome data, we constructconstructed a comprehensive soybean transcriptomic atlases. TakenTaking the investigations of genes related to blade, vascular bundles and nodule development as examples, we demonstrate that thean integrating of integrated transcriptomic atlas has robust powerful potential for in exploring key genes in organ formation. Together, the panoramic soybean transcriptomic atlases provides a valuable resource and wouldwill greatly promote the functional studystudies in the future.

Cis-regulatory elements (CREs) precisely control the spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression and chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) binding motifs controlling cell-type specification and maintenance. We identified non-cell autonomous activity of NIN-LIKE PROTEIN 7 (NLP7), the Nodule Inception (NIN) gene regulatory network and de novo enriched TF motifs in the nodule infected cells. With comprehensive developmental trajectories for endosperm and embryo, we found that 13 sucrose transporters, sharing the DOF11 binding motif, were co-up-regulated in late peripheral endosperm and identified the key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.