Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas Provart, Marius Arend, Zoran Nikoloski and Marek Mutwil ()
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Qiao Wen Tan: Nanyang Technological University
Peng Ken Lim: Nanyang Technological University
Zhong Chen: Amoeba Education Hub
Asher Pasha: University of Toronto
Nicholas Provart: University of Toronto
Marius Arend: University of Potsdam
Zoran Nikoloski: University of Potsdam
Marek Mutwil: Nanyang Technological University

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.

Date: 2023
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DOI: 10.1038/s41467-023-36517-w

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