A spatially resolved multiomic single-cell atlas of soybean development

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. We generated a comprehensive accessible chromatin and transcriptome atlas across various cell types in soybean with scATAC-seq, snRNA-seq and spatial-RNA-seq(spRNA-seq), where we collected samples from ten major tissues at different stages of the soybean life cycle. These tissues included leaf, hypocotyl, root, nodule, young pod, and five stages of developing seeds: globular stage (GS), heart stage (HS), cotyledon stage (CS), early maturation stage (EMS), and middle maturation stage (MMS). For each tissue, we conducted scATAC-seq and snRNA-seq with at least two replicates.