ArticleCell2025
A spatially resolved multi-omic single-cell atlas of soybean development.
Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Functional definition of leaf sink-to-source transition by 14C tracing reveals transcriptional reprogramming in soybean.Plant & cell physiology · 2026Article
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- Genome-Wide Identification of the Glycosyltransferase 4 Family and Characterization ofCurrent issues in molecular biology · 2026Article
- Multi-organ single-cell transcriptomic atlas identifies QrIAA14 as a candidate negative regulator of adventitious root development in Quercus robur.PLoS genetics · 2026Article
- Evaluating Causal Claims in Plant Developmental Metabolism: A When-Where-How Framework.Plants (Basel, Switzerland) · 2026Review
- Genome-Wide Identification of theGenes · 2026Article
- Single-Cell Transcriptomics Reveals the FA9-VAP Module Regulating Fatty Acid Accumulation in Soybean Seeds.Plant biotechnology journal · 2026Article
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- Single-nucleus RNA-seq and ATAC-seq analyses provide molecular insights into cadmium-stress response in alfalfa roots.Horticulture research · 2026Article
- Single-cell Transcriptome Profiling Reveals Gene Regulatory Networks and Key Genes in the Root Epidermis and Cortical Cells Associated with Early Nodulation in Glycine Max.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Epigenetic orchestration of sugar signaling in plant development and stress adaptation.Horticulture research · 2026Article
- Spatial transcriptomics reveals coordinated ventricular patterning and maturation in the developing human heart.Nature communications · 2026Article
- Omics-driven plant breeding through phenomics-enviromics crosstalk.Nature communications · 2026Review
- Power-law penalties correct distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions.NAR genomics and bioinformatics · 2026Article
- A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination.The Plant cell · 2026Article
- The potential of wheat spatial omics.Nature genetics · 2026Review
- A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination.Nature plants · 2026Article
- Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform.Nature plants · 2026Article
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9 authors.
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Abstract
Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored the conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DNA binding with one finger 11 (DOF11) motif that were co-upregulated in late peripheral endosperm, and identified 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.