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A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

Yuji Ke (UGent) , Vincent Pujol (UGent) , Jasper Staut (UGent) , Lotte Pollaris (UGent) , Ruth Seurinck (UGent) , Thomas Eekhout (UGent) , Carolin Seyfferth (UGent) , Maite Saura Sanchez (UGent) , Michiel Van Bel (UGent) , Marnik Vuylsteke (UGent) , et al.
(2025) CELL REPORTS. 44(2).
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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.
Keywords
CP: Plants, cluster annotation, gene regulatory networks, root meristem atlas, single-cell transcriptomics, untargeted spatial transcriptomics, wheat, MAIZE, EXPRESSION, REVEALS, INFERENCE, RICE, MAP

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Citation

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MLA
Ke, Yuji, et al. “A Single-Cell and Spatial Wheat Root Atlas with Cross-Species Annotations Delineates Conserved Tissue-Specific Marker Genes and Regulators.” CELL REPORTS, vol. 44, no. 2, 2025, doi:10.1016/j.celrep.2025.115240.
APA
Ke, Y., Pujol, V., Staut, J., Pollaris, L., Seurinck, R., Eekhout, T., … De Rybel, B. (2025). A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators. CELL REPORTS, 44(2). https://doi.org/10.1016/j.celrep.2025.115240
Chicago author-date
Ke, Yuji, Vincent Pujol, Jasper Staut, Lotte Pollaris, Ruth Seurinck, Thomas Eekhout, Carolin Seyfferth, et al. 2025. “A Single-Cell and Spatial Wheat Root Atlas with Cross-Species Annotations Delineates Conserved Tissue-Specific Marker Genes and Regulators.” CELL REPORTS 44 (2). https://doi.org/10.1016/j.celrep.2025.115240.
Chicago author-date (all authors)
Ke, Yuji, Vincent Pujol, Jasper Staut, Lotte Pollaris, Ruth Seurinck, Thomas Eekhout, Carolin Seyfferth, Maite Saura Sanchez, Michiel Van Bel, Marnik Vuylsteke, Andrea Ariani, Christophe Liseron-Monfils, Klaas Vandepoele, Yvan Saeys, and Bert De Rybel. 2025. “A Single-Cell and Spatial Wheat Root Atlas with Cross-Species Annotations Delineates Conserved Tissue-Specific Marker Genes and Regulators.” CELL REPORTS 44 (2). doi:10.1016/j.celrep.2025.115240.
Vancouver
1.
Ke Y, Pujol V, Staut J, Pollaris L, Seurinck R, Eekhout T, et al. A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators. CELL REPORTS. 2025;44(2).
IEEE
[1]
Y. Ke et al., “A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators,” CELL REPORTS, vol. 44, no. 2, 2025.
@article{01JKQK4WX80RMFXPNW5V6MKAXH,
  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.}},
  articleno    = {{115240}},
  author       = {{Ke, Yuji and Pujol, Vincent and Staut, Jasper and Pollaris, Lotte and Seurinck, Ruth and Eekhout, Thomas and Seyfferth, Carolin and Saura Sanchez, Maite and Van Bel, Michiel and Vuylsteke, Marnik and Ariani, Andrea and Liseron-Monfils, Christophe and Vandepoele, Klaas and Saeys, Yvan and De Rybel, Bert}},
  issn         = {{2211-1247}},
  journal      = {{CELL REPORTS}},
  keywords     = {{CP: Plants,cluster annotation,gene regulatory networks,root meristem atlas,single-cell transcriptomics,untargeted spatial transcriptomics,wheat,MAIZE,EXPRESSION,REVEALS,INFERENCE,RICE,MAP}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{16}},
  title        = {{A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators}},
  url          = {{http://doi.org/10.1016/j.celrep.2025.115240}},
  volume       = {{44}},
  year         = {{2025}},
}
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