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| Status |
Public on Jan 06, 2025 |
| Title |
A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes |
| Organism |
Triticum aestivum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Despite the broad use of single-cell and single-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, using soil-grown wheat roots as a model, we generated a single-cell RNA-sequencing (scRNA-seq) atlas and annotated cluster identities in an unbiased way by transferring existing annotations from publicly available datasets in wheat, rice, maize and Arabidopsis. These cross-species orthology-based predictions were next validated using untargeted spatial transcriptomics. This information refined existing cluster annotations for different datasets across key plant model species. We then used the validated clusters to generate cell type-specific gene regulatory networks for root tissues of wheat and two other monocot crop species. By integrating all available data, including homeolog expression in wheat, we predicted reliable tissue-specific markers which are conserved across different species. In summary, we provided an annotated and validated single cell transcriptomic resource for soil-grown wheat root apical meristems and revealed conserved cell type-specific regulators and markers across species. These data expand upon previous root single cell atlas resources in crops, and will facilitate cell type annotation in non-model plant species in the future.
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| Overall design |
Single-cell RNA-seq experiments were performed on protoplasts extracted from soil-grown wheat roots.
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| Contributor(s) |
Ke Y, Pujol V, Staut J, Pollaris L, Seurinck R, Eekhout T, Vuylsteke M, Saura-Sanchez MT, Grones C, Van Bel M, Ariani A, Liseron-Monfils C, Vandepoele K, Saeys Y, De Rybel B |
| Citation(s) |
39893633 |
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| Submission date |
Jun 20, 2024 |
| Last update date |
Mar 13, 2025 |
| Contact name |
Bert De Rybel |
| E-mail(s) |
beryb@psb.vib-ugent.be
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| Organization name |
VIB
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| Department |
Center for Plant Systems Biology
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| Lab |
Vascular Development
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| Street address |
Technologiepark 71
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| City |
Ghent |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
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| Platforms (1) |
| GPL25409 |
Illumina NovaSeq 6000 (Triticum aestivum) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA1126233 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE270342_RAW.tar |
254.6 Mb |
(http)(custom) |
TAR (of H5) |
| GSE270342_seuratObj_for_publication.rds.gz |
557.3 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
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