Comparative Transcriptomic Analysis of <i>Zymoseptoria tritici</i> Reveals Interaction-Specific Gene Expression Patterns During Susceptible, Resistant, and Nonhost Interactions

<i>Zymoseptoria tritici</i> causes Septoria tritici blotch, which significantly reduces yields of wheat. To investigate infection phase-specific gene expression in the pathogen, we analyzed gene expression during infection of susceptible and resistant wheat cultivars, as well as the nonhost species barley, at 1, 3, 6, 10, 17, and 23 days postinoculation (DPI). There were dramatic differences in pathogen gene expression at 10 DPI in the susceptible compared with both resistant interactions. The most pronounced differences in pathogen gene expression were observed at 3 DPI in both the susceptible and resistant host interactions compared with the nonhost. Thirty-one putative effectors showed early expression during the susceptible compared with the nonhost interaction; six were selected for subcellular localization studies. Using <i>Agrobacterium</i>-mediated transient expression in <i>Nicotiana benthamiana</i>, subcellular localization assays revealed that two candidate effectors localized to putative mobile cytosolic bodies when expressed without their signal peptides, suggesting potential roles in intracellular signaling or host gene regulation. When expressed with their signal peptides, four candidate effectors localized to the cytosol, whereas one did not accumulate to detectable levels. Comparison of pathogen gene expression in the susceptible host with expression in the resistant hosts identified genes expressed during the transition from biotrophic to necrotrophic growth at 10 DPI. Comparison of pathogen gene expression in resistant and susceptible hosts, versus in the nonhost barley, identified genes involved in initial colonization and host recognition. These results contribute to understanding candidate effectors that are activated early during infection and may play a role in the suppression of plant immunity. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.