Integrated single-cell transcriptomics and spatial metabolomics unveil cellular differentiation and ginsenosides biosynthesis in Panax root tips

Abstract Root tips, which represent the initial stage of taproot development, serve as an ideal model for investigating plant growth and secondary metabolism. However, studies of root tips in Panax species have been limited, restricting our understanding of cell fate transitions during early root development and the cellular heterogeneity associated with ginsenosides biosynthesis. To address this gap, we conducted single-cell RNA sequencing (scRNA-seq) and spatial metabolomics analyses on the root tips of three Panax species: Panax notoginseng, Panax ginseng, and Panax quinquefolium. Our research reconstructed the developmental trajectory of the early endodermis and revealed epidermis-specific expression patterns of key enzyme genes involved in ginsenosides biosynthesis. We identified several novel transcription factors (TFs): IAA29 (which positively regulates endodermis suberization) and MYB2/MYB78 (positive regulators of ginsenosides biosynthesis), validated by dual-LUC reporter and electrophoretic mobility shift assay (EMSA). Conserved and divergent ligand-receptor interaction patterns across the three Panax species were discovered, with the FAD gene family exhibiting tissue- and species-specific expression. Cell-specific genes expression was confirmed by RNA in situ hybridization. Mass spectrometry imaging (MSI) mapped ginsenosides spatial distribution, while LC–MS/MS verified species-specific biosynthesis. This study presents a single-cell transcriptional landscape of early differentiation and cell type-specific ginsenosides accumulation in the Panax genus.

• Publication year

  2025

• Venue

  Horticulture Research

• Publication date

  2025-07-31

• Fields of study

  Biology, Medicine, Chemistry, Environmental Science

• Identifiers
  DOI 10.1093/hr/uhaf202PMID 41180020PMCID 12574545
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2022influential reference
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  2021cited by this paper
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  2021cited by this paper
• Ginsenosides in Panax genus and their biosynthesis

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• Single‐cell RNA sequencing profiles of stem‐differentiating xylem in poplar

  2021cited by this paper
• SUBERMAN Regulates Developmental Suberization of the Arabidopsis Root Endodermis.

  2020cited by this paper
• The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis

  2020cited by this paper
• Single-Cell Resolution of Lineage Trajectories in the Arabidopsis Stomatal Lineage and Developing Leaf

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• Advances in Saponin Diversity of Panax ginseng

  2020cited by this paper
• A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants

  2020cited by this paper
• Understanding the consequence of environmental stress for accumulation of secondary metabolites in medicinal and aromatic plants

  2020cited by this paper
• Advances in Ginsenosides

  2020cited by this paper
• Traditional uses, chemical diversity and biological activities of Panax L. (Araliaceae): A review.

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• Stress and defense responses in plant secondary metabolites production

  2019cited by this paper
• A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and response

  2019cited by this paper
• Generalizing RNA velocity to transient cell states through dynamical modeling

  2019influential reference
• PlantRegMap: charting functional regulatory maps in plants

  2019cited by this paper
• Faculty Opinions recommendation of Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells.

  2019cited by this paper
• Metabolomes and transcriptomes revealed the saponin distribution in root tissues of Panax quinquefolius and Panax notoginseng

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• Transcriptomic profiling reveals MEP pathway contributing to ginsenoside biosynthesis in Panax ginseng

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• A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root.

  2019cited by this paper
• Fast, sensitive, and accurate integration of single cell data with Harmony

  2019influential reference
• High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

  2019cited by this paper
• Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing.

  2019cited by this paper
• Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells1[OPEN]

  2019cited by this paper
• DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors

  2018influential reference
• Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

  2018cited by this paper
• Integrating single-cell transcriptomic data across different conditions, technologies, and species

  2018influential reference
• Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng

  2018influential reference
• RNA velocity of single cells

  2018influential reference
• Receptor Kinase THESEUS1 Is a Rapid Alkalinization Factor 34 Receptor in Arabidopsis.

  2018cited by this paper
• Integrated metabolomic and transcriptomic analyses revealed the distribution of saponins in Panax notoginseng

  2018cited by this paper
• Regulation of intercellular TARGET OF MONOPTEROS 7 protein transport in the Arabidopsis root

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• Reversed graph embedding resolves complex single-cell trajectories

  2017influential reference
• iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases.

  2016cited by this paper
• MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root

  2015cited by this paper
• The MYB36 transcription factor orchestrates Casparian strip formation

  2015cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

  2013influential reference
• STAR: ultrafast universal RNA-seq aligner

  2013influential reference
• Plant stem cell niches.

  2012cited by this paper
• clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

  2012cited by this paper
• Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

  2009cited by this paper
• Mfuzz: A software package for soft clustering of microarray data

  2007influential reference
• Plant stem cell niches.

  2005cited by this paper

• Single-nucleus RNA-sequencing reveals the cellular programs driving nematode-induced giant cell formation in tomato

  2025cites this paper