A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators
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.
Authors
- Andrea Ariani (ORCID: https://orcid.org/0000-0002-3356-5329)
- Yvan Saeys (ORCID: https://orcid.org/0000-0002-0415-1506)
- Vincent Pujol (ORCID: https://orcid.org/0000-0001-9903-3475)
- Bert De Rybel (ORCID: https://orcid.org/0000-0002-9551-042X)
- Thomas Eekhout (ORCID: https://orcid.org/0000-0002-2878-1553)
- Michiel Van Bel (ORCID: https://orcid.org/0000-0002-1873-2563)
- Christophe Liseron-Monfils (ORCID: https://orcid.org/0000-0002-9024-0555)
- Jasper Staut (ORCID: https://orcid.org/0000-0001-5197-337X)
- Klaas Vandepoele (ORCID: https://orcid.org/0000-0003-4790-2725)
- Yuji Ke (ORCID: https://orcid.org/0000-0002-8175-7878)
- Maite Saura-Sánchez (ORCID: https://orcid.org/0000-0001-8115-3540)
- Marnik Vuylsteke (ORCID: https://orcid.org/0000-0001-5145-6460)
- Ruth Seurinck (ORCID: https://orcid.org/0000-0002-6636-7572)
- Lotte Pollaris (ORCID: https://orcid.org/0000-0002-9509-9386)
- Carolin Grones
Institutions
- Ghent University (BE)
- VIB-UGent Center for Plant Systems Biology (BE)
- VIB-UGent Center for Inflammation Research (BE)
- VIB Single Cell Core
Publication Details
- Journal
- Cell Reports
- Published
- 2025-02-01
- DOI
- https://doi.org/10.1016/j.celrep.2025.115240
- Citations
- 21
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 16.93
Funders
- Agentschap Innoveren en Ondernemen
- Fonds Wetenschappelijk Onderzoek
- Universiteit Gent
- Vlaamse regering
- Bijzonder Onderzoeksfonds UGent
- H2020 European Research Council