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Peer-reviewedCC BY-NC-NDNature Communications

Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots

  • Guannan Wang1,2,3,4
  • Kook Hui Ryu5,6
  • Andrea Dinneny2,3,4
  • Jiyoung Lee7,8
  • Dong‐Ha Oh1,9
  • Prashanth Ramachandran2,3,10
  • Marina Oliva11,12
  • Ryan Lister11,13,14
  • José R. Dinneny15,16,17
  • John Schiefelbein18,4
  • Maheshi Dassanayake19,6
19 affiliations
  1. 1Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
  2. 2Department of Biology, Stanford University, Stanford, CA, USA
  3. 3Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
  4. 4Stanford University
  5. 5Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
  6. 6University of Michigan
  7. 7Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
  8. 8DOE Joint Genome Institute
  9. 9Joint Genome Institute
  10. 10Virginia Tech
  11. 11ARC Centres of Excellence in Plant Energy Biology and Plants for Space, School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
  12. 12Louisiana State University
  13. 13The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
  14. 14University of Western Australia
  15. 15Department of Biology, Stanford University, Stanford, CA, USA. [email protected]
  16. 16Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. [email protected]
  17. 17The University of Western Australia
  18. 18Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA. [email protected]
  19. 19Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA. [email protected]
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Abstract

Plants are composed of diverse cell types that facilitate adaptations to the environment, yet cross-species comparisons of such response programs at single-cell resolution remain scarce. To explore this diversity, here we profile >200,000 root cells from five Brassicaceae species, including stress-sensitive species (Arabidopsis thaliana, Sisymbrium irio), extremophytes (Eutrema salsugineum, Schrenkiella parvula), and the polyploid crop Camelina sativa under control, NaCl, and abscisic acid (ABA) treatments. We develop a computational pipeline to characterize the conservation and divergence of cell-type gene expression across the Brassicaceae, revealing that approximately half of previously defined Arabidopsis cell-type markers fail to maintain conserved expression in one or more non-Arabidopsis species. Therefore, we curate a refined set of pan-Brassicaceae markers and identify orthologs whose expression profiles have diverged across lineages. Using in situ hybridization, we map distinct cortex subpopulations to specific cortical layers across species, and find flavonoid biosynthesis programs preferentially localized to the inner cortex layer, linking cortex-layer specification to metabolic specialization. Cell-type contributions to stress responses differ among species and across treatments, with lineage-specific losses of responsiveness occurring less frequently but evolutionarily more favored than lineage-specific gains. In C. sativa, sub-genomes contribute equally to stress responses, and homeologs with divergent responses typically lack other signatures of functional divergence. Together, this work establishes a foundational root single-cell atlas and an analytical framework for multi-species comparative transcriptomics, providing insights into how stress responses diversify across cell types, stress-sensitive to stress-adapted species, and in crop lineages.

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Cite

BibTeXRIS
BibTeX
@article{wang2026evolutionary,
  title = {{Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots}},
  author = {Guannan Wang and Kook Hui Ryu and Andrea Dinneny and Jiyoung Lee and Dong‐Ha Oh and Prashanth Ramachandran and Marina Oliva and Ryan Lister and José R. Dinneny and John Schiefelbein and Maheshi Dassanayake},
  journal = {Nature Communications},
  year = {2026},
  month = may,
  doi = {10.1038/s41467-026-73270-2},
  url = {https://doi.org/10.1038/s41467-026-73270-2},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots
AU  - Guannan Wang
AU  - Kook Hui Ryu
AU  - Andrea Dinneny
AU  - Jiyoung Lee
AU  - Dong‐Ha Oh
AU  - Prashanth Ramachandran
AU  - Marina Oliva
AU  - Ryan Lister
AU  - José R. Dinneny
AU  - John Schiefelbein
AU  - Maheshi Dassanayake
PY  - 2026
DA  - 2026/05/20
JO  - Nature Communications
DO  - 10.1038/s41467-026-73270-2
UR  - https://doi.org/10.1038/s41467-026-73270-2
AB  - Plants are composed of diverse cell types that facilitate adaptations to the environment, yet cross-species comparisons of such response programs at single-cell resolution remain scarce. To explore this diversity, here we profile >200,000 root cells from five Brassicaceae species, including stress-sensitive species (Arabidopsis thaliana, Sisymbrium irio), extremophytes (Eutrema salsugineum, Schrenkiella parvula), and the polyploid crop Camelina sativa under control, NaCl, and abscisic acid (ABA) treatments. We develop a computational pipeline to characterize the conservation and divergence of cell-type gene expression across the Brassicaceae, revealing that approximately half of previously defined Arabidopsis cell-type markers fail to maintain conserved expression in one or more non-Arabidopsis species. Therefore, we curate a refined set of pan-Brassicaceae markers and identify orthologs whose expression profiles have diverged across lineages. Using in situ hybridization, we map distinct cortex subpopulations to specific cortical layers across species, and find flavonoid biosynthesis programs preferentially localized to the inner cortex layer, linking cortex-layer specification to metabolic specialization. Cell-type contributions to stress responses differ among species and across treatments, with lineage-specific losses of responsiveness occurring less frequently but evolutionarily more favored than lineage-specific gains. In C. sativa, sub-genomes contribute equally to stress responses, and homeologs with divergent responses typically lack other signatures of functional divergence. Together, this work establishes a foundational root single-cell atlas and an analytical framework for multi-species comparative transcriptomics, providing insights into how stress responses diversify across cell types, stress-sensitive to stress-adapted species, and in crop lineages.
SN  - 2041-1723
ER  -