A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators
Summary: 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 a...
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| Language: | English |
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Elsevier
2025-02-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124725000117 |
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| author | Yuji Ke Vincent Pujol Jasper Staut Lotte Pollaris Ruth Seurinck Thomas Eekhout Carolin Grones Maite Saura-Sanchez Michiel Van Bel Marnik Vuylsteke Andrea Ariani Christophe Liseron-Monfils Klaas Vandepoele Yvan Saeys Bert De Rybel |
| author_facet | Yuji Ke Vincent Pujol Jasper Staut Lotte Pollaris Ruth Seurinck Thomas Eekhout Carolin Grones Maite Saura-Sanchez Michiel Van Bel Marnik Vuylsteke Andrea Ariani Christophe Liseron-Monfils Klaas Vandepoele Yvan Saeys Bert De Rybel |
| author_sort | Yuji Ke |
| collection | DOAJ |
| description | Summary: 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. |
| format | Article |
| id | doaj-art-34237849ff4546639584f2263d2c3768 |
| institution | Kabale University |
| issn | 2211-1247 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-34237849ff4546639584f2263d2c37682025-02-03T04:16:40ZengElsevierCell Reports2211-12472025-02-01442115240A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulatorsYuji Ke0Vincent Pujol1Jasper Staut2Lotte Pollaris3Ruth Seurinck4Thomas Eekhout5Carolin Grones6Maite Saura-Sanchez7Michiel Van Bel8Marnik Vuylsteke9Andrea Ariani10Christophe Liseron-Monfils11Klaas Vandepoele12Yvan Saeys13Bert De Rybel14Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, BelgiumDepartment of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, BelgiumDepartment of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, BelgiumDepartment of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB Single Cell Core, VIB, Ghent/Leuven, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, BelgiumGnomixx, Melle, BelgiumBASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, BelgiumBASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Corresponding authorDepartment of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, BE, Belgium; Corresponding authorDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2211124725000117CP: Plants |
| spellingShingle | Yuji Ke Vincent Pujol Jasper Staut Lotte Pollaris Ruth Seurinck Thomas Eekhout Carolin Grones Maite Saura-Sanchez Michiel Van Bel Marnik Vuylsteke Andrea Ariani Christophe Liseron-Monfils Klaas Vandepoele Yvan Saeys Bert De Rybel A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators Cell Reports CP: Plants |
| title | A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators |
| title_full | A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators |
| title_fullStr | A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators |
| title_full_unstemmed | A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators |
| title_short | A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators |
| title_sort | single cell and spatial wheat root atlas with cross species annotations delineates conserved tissue specific marker genes and regulators |
| topic | CP: Plants |
| url | http://www.sciencedirect.com/science/article/pii/S2211124725000117 |
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