ArticlePlant communications2024
Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism.
Article in Plant communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass.ACS omega · 2026Article
- Benchmarking plant single cell RNA-sequencing sample processing strategies.The EMBO journal · 2026Article
- Review
- A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum.The Plant journal : for cell and molecular biology · 2026Article
- Metabolomic and Single-Cell Transcriptomic Analyses Shed Light on Secondary Metabolite Profiling and Potential Developmental Dynamics of Glandular Trichomes in Artemisia argyi.Plant biotechnology journal · 2026Article
- Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.Genome biology · 2026Article
- Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives.Briefings in functional genomics · 2026Review
- Integrated single cell transcriptomics analysis for unraveling heterogeneity and plasticity of root cells for sustainable and regenerative agriculture.Frontiers in plant science · 2026Review
- Integrated single-cell transcriptomics and spatial metabolomics unveil cellular differentiation and ginsenosides biosynthesis inHorticulture research · 2025Article
- Unearthing the hidden organ: vital role of the root in drought tolerance of plants.Plant molecular biology · 2025Review
- Single-cell omics in plant biology: mechanistic insights and applications for crop improvement.Advanced biotechnology · 2025Review
- MicroRNA control of stem cell reconstitution and growth in root regeneration.Nature plants · 2025Article
- Roles of maizeFrontiers in plant science · 2025Article
- Single-Cell Transcriptomics Applied in Plants.Cells · 2024Review
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5 authors.
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Abstract
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
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