ArticleNature plants2025
A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle.
Article in Nature plants, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Inferring cell division from cell shape.The Plant cell · 2026Article
- A spatiotemporal single-cell transcriptomic atlas reveals fertilization-induced auxin signaling driving strawberry fruit set and development.Nature communications · 2026Article
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- Evaluating Causal Claims in Plant Developmental Metabolism: A When-Where-How Framework.Plants (Basel, Switzerland) · 2026Review
- Multi-Omics Frontiers in Plant Adaptation and Growth: From Molecular Networks to Precision Breeding.Plants (Basel, Switzerland) · 2026Article
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- Shaping Plant Adaptation in a Warmer World: Developmental Plasticity Under Moderately Elevated Temperatures.Plants (Basel, Switzerland) · 2026Review
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- SNc Nuclease GenesInternational journal of molecular sciences · 2026Article
- Time- and space-resolved transcriptional regulation in Arabidopsis thaliana.Plant biology (Stuttgart, Germany) · 2026Article
- Transient cell states encode positional information to direct asymmetric growth.bioRxiv : the preprint server for biology · 2026Article
- Cell-specific dedifferentiation inbioRxiv : the preprint server for biology · 2026Article
- A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination.The Plant cell · 2026Article
- Single-nucleus transcriptome profiling unveils cell-type-specific ethylene and TOR signaling in tomato.Horticulture research · 2026Article
- Cell-type-specific gating of gene regulatory modules as a hallmark of early immune responses in Arabidopsis leaves.The New phytologist · 2026Article
- A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination.Nature plants · 2026Article
- Advances in seed omics.Journal of experimental botany · 2026Review
- The Floral Bottleneck in a Changing Climate: Molecular Mechanisms, Knowledge Gaps, and Future Directions.International journal of molecular sciences · 2026Review
- Decoding plant physiology through systems biology: Integrative multi-omics and computational perspectives for next-generation crop design.Plant communications · 2026Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Arabidopsis has been pivotal in uncovering fundamental principles of plant biology, yet a comprehensive, high-resolution understanding of its cellular identities throughout the entire life cycle remains incomplete. Here we present a single-nucleus and spatial transcriptomic atlas spanning ten developmental stages, encompassing over 400,000 nuclei from all organ systems and tissues-from seeds to developing siliques. Leveraging paired single-nucleus and spatial transcriptomic datasets, we annotate 75% of identified cell clusters, revealing striking molecular diversity in cell types and states across development. Our integrated approach identified conserved transcriptional signatures among recurrent cell types, organ-specific heterogeneity and previously uncharacterized cell-type-specific markers validated spatially. Moreover, we uncover dynamic transcriptional programs governing secondary metabolite production and differential growth patterns, exemplified by detailed spatial profiling of the compact yet complex apical hook structure; this profiling revealed transient cellular states linked to developmental progression and hormonal regulation, highlighting the hidden complexity underlying plant morphogenesis. Functional validation of genes uniquely expressed within specific cell contexts confirmed their essential developmental roles, underscoring the predictive power of our atlas. Collectively, this comprehensive resource provides an invaluable foundation for exploring cellular differentiation, environmental responses and genetic perturbations at high resolution, advancing our understanding of plant biology.
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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.