Abstract Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species for PTI responses to the MAMP flg22, we identified a set of genes with expression changes under purifying selection in the Brassicaceae species and genes exhibiting species-specific expression signatures. Variation in flg22-triggered transcriptome and metabolome responses across Brassicaceae species was incongruent with their phylogeny while expression changes were strongly conserved within A. thaliana , suggesting directional selection for some species-specific gene expression. We found the enrichment of WRKY transcription factor binding sites in 5’-regulatory regions in conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene responses in PTI. Our findings advance our understanding of transcriptome evolution during biotic stress.

Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species