Kingdom-wide comparative transcriptomics reveals deeply conserved and predictable stress response programs across Viridiplantae

Abstract

How conserved stress responses are across the plant kingdom remains poorly understood. Here, we present a kingdom-wide stress transcriptome atlas of 36 Viridiplantae species, from chlorophytes to angiosperms, across nine abiotic and biotic stresses. The atlas integrates reanalyzed public RNA-seq data with new in-house stress experiments on three species representing basal lineages, yielding 13.6 million differential expression calls from over 3,200 manually curated control-treatment comparisons. We find that ancient gene families respond broadly but moderately, while lineage-specific families respond narrowly but intensely, revealing a division of labor in stress gene deployment. Stress response conservation decays with phylogenetic distance yet remains detectable across more than 700 million years of divergence, with upregulated genes diverging faster than downregulated genes. Functional co-occurrence analysis uncovers a deeply conserved growth-defence tradeoff alongside stress-specific transcriptional rewiring. Conserved stress co-expression modules undergo regulatory subfunctionalization through duplication, with whole-genome duplicate pairs preferentially retained within modules. Finally, DNA and RNA foundation models predict stress responsiveness from sequence alone (auROC 0.755), suggesting a partially conserved cis-regulatory code underlying stress responses across the kingdom.