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Peer-reviewedCC BY 4.0Proceedings of the National Academy of Sciences of the United States of America

Biotic response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations

  • Ana Paula Leite Montalvão1
  • Kevin D. Murray1
  • Ilja Bezrukov1
  • Natalie Betz1
  • Lucas P. Henry2,3
  • Paloma Duran4
  • Patrick Boppert1
  • Martina Kolb1
  • TEAM PATHOCOM
  • Fabrice Roux4
  • Joy Bergelson2,3
  • Detlef Weigel1,5
1 more authors
  • Wei Yuan1
5 affiliations
  1. 1Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
  2. 2Department of Biology, New York University, New York, NY 10003
  3. 3Center for Genomics and Systems Biology, New York University, New York, NY 10003
  4. 4Laboratoire des Interactions Plantes-Microrganismes, CNRS, Institut national de recherche pour l‘agriculture, l‘alimentation et l‘environnement, Université de Toulouse, Castanet Tolosan 31326, France
  5. 5Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72076, Germany
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Abstract

Extensive laboratory experimentation has revealed conserved molecular pathways controlling growth and stress responses in plants, yet how these programs operate in natural settings remains poorly understood. We have investigated the organization of the transcriptome in wild populations of Arabidopsis thaliana by sampling plants across 60 natural sites in Europe and North America over two seasons. Transcriptomes varied extensively among individuals and were only weakly structured by geography or season. No groups of plants stood out due to clear biotic or abiotic stress signatures known from the laboratory. While only a small portion of transcriptome variance was explained by disease symptoms or environmental and phenotypic variables, infection-associated signals accounted for the largest share of the explainable fraction. Biotic-response networks identified in controlled laboratory conditions were well conserved in wild transcriptomes, while other networks, including abiotic-response networks were substantially reorganized in wild plants. Together, these results indicate that while certain transcriptional modules are easily reidentified when moving from the wild to controlled conditions, many regulatory relationships differ in these two contexts, highlighting how ecological complexity shapes transcriptome organization in natural populations.

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Cite

BibTeXRIS
BibTeX
@article{montalvao2026biotic,
  title = {{Biotic response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations}},
  author = {Ana Paula Leite Montalvão and Kevin D. Murray and Ilja Bezrukov and Natalie Betz and Lucas P. Henry and Paloma Duran and Patrick Boppert and Martina Kolb and TEAM PATHOCOM and Fabrice Roux and Joy Bergelson and Detlef Weigel and Wei Yuan},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  year = {2026},
  month = oct,
  doi = {10.1073/pnas.2611539123},
  url = {https://doi.org/10.1073/pnas.2611539123},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Biotic response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations
AU  - Ana Paula Leite Montalvão
AU  - Kevin D. Murray
AU  - Ilja Bezrukov
AU  - Natalie Betz
AU  - Lucas P. Henry
AU  - Paloma Duran
AU  - Patrick Boppert
AU  - Martina Kolb
AU  - TEAM PATHOCOM
AU  - Fabrice Roux
AU  - Joy Bergelson
AU  - Detlef Weigel
AU  - Wei Yuan
PY  - 2026
DA  - 2026/10/19
JO  - Proceedings of the National Academy of Sciences of the United States of America
DO  - 10.1073/pnas.2611539123
UR  - https://doi.org/10.1073/pnas.2611539123
AB  - Extensive laboratory experimentation has revealed conserved molecular pathways controlling growth and stress responses in plants, yet how these programs operate in natural settings remains poorly understood. We have investigated the organization of the transcriptome in wild populations of Arabidopsis thaliana by sampling plants across 60 natural sites in Europe and North America over two seasons. Transcriptomes varied extensively among individuals and were only weakly structured by geography or season. No groups of plants stood out due to clear biotic or abiotic stress signatures known from the laboratory. While only a small portion of transcriptome variance was explained by disease symptoms or environmental and phenotypic variables, infection-associated signals accounted for the largest share of the explainable fraction. Biotic-response networks identified in controlled laboratory conditions were well conserved in wild transcriptomes, while other networks, including abiotic-response networks were substantially reorganized in wild plants. Together, these results indicate that while certain transcriptional modules are easily reidentified when moving from the wild to controlled conditions, many regulatory relationships differ in these two contexts, highlighting how ecological complexity shapes transcriptome organization in natural populations.
SN  - 0027-8424
SN  - 1091-6490
ER  -