Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics
- Author
- Rubén Tenorio Berrio (UGent) , Eline Verhelst (UGent) , Thomas Eekhout (UGent) , Carolin Seyfferth (UGent) , Lieven De Veylder (UGent) , Bert De Rybel (UGent) and Marieke Dubois (UGent)
- Organization
- Project
- Abstract
- Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step toward engineering improved drought resilience. However, the molecular responses to drought are complex as they depend on multiple factors, including the severity of drought, the profiled organ, its developmental stage or even the cell types therein. Thus, deciphering the transcriptional responses to drought is especially challenging. In this study, we investigated tissue-specific responses to mild drought (MD) in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve transcriptional integrity during cell isolation, we inhibited RNA synthesis using the transcription inhibitor actinomycin D, and demonstrated the benefits of transcriptome fixation for studying mild stress responses at a single-cell level. We present a curated and validated single-cell atlas, comprising 50 797 high-quality cells from almost all known cell types present in the leaf. All cell type annotations were validated with a new library of reporter lines. The curated data are available to the broad community in an intuitive tool and a browsable single-cell atlas (http://www.single-cell.be/plant/leaf-drought). We show that the mesophyll contains two spatially separated cell populations with distinct responses to drought: one enriched in canonical abscisic acid-related drought-responsive genes, and another one enriched in genes involved in iron starvation responses. Our study thus reveals a dual adaptive mechanism of the leaf mesophyll in response to MD and provides a valuable resource for future research on stress responses.
- Keywords
- Arabidopsis thaliana, drought, leaf, mesophyll, single‐cell RNA sequencing, transcriptome changes, GENE-EXPRESSION, LOW-TEMPERATURE, IRON HOMEOSTASIS, THALIANA COR15A, PLANT-GROWTH, WATER, STRESS, ACTINOMYCIN, ACTIVATORS, TOLERANCE
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table S1 primers.xlsx
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table S2 protoplastingresponse clustering.xlsx
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table S4 normalizedbulk transcriptome.xlsx
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table S5 droughtresponses.xlsx
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table S7 pseudobulk digestionmaintissue.xlsx
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table S9 drought mesophyll.xlsx
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New Phytologist - 2025 - Tenorio Berrío - Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll.pdf
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01JPTR5QP7736GTGSVKCHQA6K5
- MLA
- Tenorio Berrio, Rubén, et al. “Dual and Spatially Resolved Drought Responses in the Arabidopsis Leaf Mesophyll Revealed by Single‐cell Transcriptomics.” NEW PHYTOLOGIST, vol. 246, no. 3, 2025, pp. 840–58, doi:10.1111/nph.20446.
- APA
- Tenorio Berrio, R., Verhelst, E., Eekhout, T., Seyfferth, C., De Veylder, L., De Rybel, B., & Dubois, M. (2025). Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics. NEW PHYTOLOGIST, 246(3), 840–858. https://doi.org/10.1111/nph.20446
- Chicago author-date
- Tenorio Berrio, Rubén, Eline Verhelst, Thomas Eekhout, Carolin Seyfferth, Lieven De Veylder, Bert De Rybel, and Marieke Dubois. 2025. “Dual and Spatially Resolved Drought Responses in the Arabidopsis Leaf Mesophyll Revealed by Single‐cell Transcriptomics.” NEW PHYTOLOGIST 246 (3): 840–58. https://doi.org/10.1111/nph.20446.
- Chicago author-date (all authors)
- Tenorio Berrio, Rubén, Eline Verhelst, Thomas Eekhout, Carolin Seyfferth, Lieven De Veylder, Bert De Rybel, and Marieke Dubois. 2025. “Dual and Spatially Resolved Drought Responses in the Arabidopsis Leaf Mesophyll Revealed by Single‐cell Transcriptomics.” NEW PHYTOLOGIST 246 (3): 840–858. doi:10.1111/nph.20446.
- Vancouver
- 1.Tenorio Berrio R, Verhelst E, Eekhout T, Seyfferth C, De Veylder L, De Rybel B, et al. Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics. NEW PHYTOLOGIST. 2025;246(3):840–58.
- IEEE
- [1]R. Tenorio Berrio et al., “Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics,” NEW PHYTOLOGIST, vol. 246, no. 3, pp. 840–858, 2025.
@article{01JPTR5QP7736GTGSVKCHQA6K5,
abstract = {{Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step toward engineering improved drought resilience. However, the molecular responses to drought are complex as they depend on multiple factors, including the severity of drought, the profiled organ, its developmental stage or even the cell types therein. Thus, deciphering the transcriptional responses to drought is especially challenging. In this study, we investigated tissue-specific responses to mild drought (MD) in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve transcriptional integrity during cell isolation, we inhibited RNA synthesis using the transcription inhibitor actinomycin D, and demonstrated the benefits of transcriptome fixation for studying mild stress responses at a single-cell level. We present a curated and validated single-cell atlas, comprising 50 797 high-quality cells from almost all known cell types present in the leaf. All cell type annotations were validated with a new library of reporter lines. The curated data are available to the broad community in an intuitive tool and a browsable single-cell atlas (http://www.single-cell.be/plant/leaf-drought). We show that the mesophyll contains two spatially separated cell populations with distinct responses to drought: one enriched in canonical abscisic acid-related drought-responsive genes, and another one enriched in genes involved in iron starvation responses. Our study thus reveals a dual adaptive mechanism of the leaf mesophyll in response to MD and provides a valuable resource for future research on stress responses.}},
author = {{Tenorio Berrio, Rubén and Verhelst, Eline and Eekhout, Thomas and Seyfferth, Carolin and De Veylder, Lieven and De Rybel, Bert and Dubois, Marieke}},
issn = {{0028-646X}},
journal = {{NEW PHYTOLOGIST}},
keywords = {{Arabidopsis thaliana,drought,leaf,mesophyll,single‐cell RNA sequencing,transcriptome changes,GENE-EXPRESSION,LOW-TEMPERATURE,IRON HOMEOSTASIS,THALIANA COR15A,PLANT-GROWTH,WATER,STRESS,ACTINOMYCIN,ACTIVATORS,TOLERANCE}},
language = {{eng}},
number = {{3}},
pages = {{840--858}},
title = {{Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics}},
url = {{http://doi.org/10.1111/nph.20446}},
volume = {{246}},
year = {{2025}},
}
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