ArticleCell reports2025
A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators.
Article in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Integrating cross-omics research through FAIR Digital Objects with DataPLANT.Journal of integrative bioinformatics · 2026Article
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- Wheat's war against stripe rust: Integrating host immunity, genomics and breeding for durable resistance.The plant genome · 2026Review
- Benchmarking plant single cell RNA-sequencing sample processing strategies.The EMBO journal · 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
- A multi-branched EMS mutant of Isodon lophanthoides var. graciliflorus exhibits significant differences in phytohormones and diterpenoids.BMC plant biology · 2026Article
- Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.Genome biology · 2026Article
- Integrated experimental and computational workflows for single-cell transcriptomics in plants.Plant methods · 2026Article
- Integrated single cell transcriptomics analysis for unraveling heterogeneity and plasticity of root cells for sustainable and regenerative agriculture.Frontiers in plant science · 2026Review
- Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development.Nature plants · 2026Article
- Wheat Plasma Membrane Receptors: Orchestrating Immunity and Bridging to Crop Improvement.Current issues in molecular biology · 2025Review
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Towards smart agriculture: AI-driven prediction of key genes for revolutionizing crop breeding.Planta · 2025Review
- The impact of asymmetrical gene expression on the development of spike morphology iniMetaOmics · 2025Article
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Authors and funding
15 authors.
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Abstract
Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation in less-studied plant species remains a major challenge due to the lack of validated marker genes. Here, we generated a single-cell RNA sequencing atlas of soil-grown wheat roots and annotated cluster identities by transferring annotations from publicly available datasets in wheat, rice, maize, and Arabidopsis. The predictions from our orthology-based annotation approach were next validated using untargeted spatial transcriptomics. These results allowed us to predict evolutionarily conserved tissue-specific markers and generate cell type-specific gene regulatory networks for root tissues of wheat and the other species used in our analysis. In summary, we generated a single-cell and spatial transcriptomics resource for wheat root apical meristems, including numerous known and uncharacterized cell type-specific marker genes and developmental regulators. These data and analyses will facilitate future cell type annotation in non-model plant species.
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