Disease resistance in cypress involves a dynamic transcriptome-wide response that includes resistance genes characterized in model pathosystems

Abstract Cypress Canker Disease (CCD) is a tree pandemic caused by fungi of the genus Seiridium . Among the Cupressaceae, Cupressus sempervirens is a main host of CCD. Although breeding programs identified CCD-resistant C. sempervirens clones, molecular mechanisms conferring resistance still need to be clarified. Here, we present the first transcriptomic analyses of the S. cardinale-C. sempervirens pathosystem using a dual RNA-seq approach across resistant and susceptible clones 3, 15, and 30 days post pathogen-inoculation. An early and sustained transcriptional activation was observed in resistant clones, characterized by higher numbers of differentially expressed genes than in susceptible clones. Notably, putative resistance genes such as Roq1, RUN1, TAO1 and RPV1 were observed in Cupressus for the first time. These genes, together with stress-related genes and transporters, were up-regulated in resistant clones. Host clonality facilitated the identification of candidate resistance-associated gene homologs and of gene subsets whose temporal expression patterns suggest dynamic roles during disease progression. Differential expression between wounded and fungus-inoculated tissues helped to describe responses linked to wounding from those specific to infection. Our findings suggest that CCD resistance might integrate stress responses, signaling, and R-gene homologs. These genes represent candidate biomarkers of resistance that warrant further validation across broader cypress populations and pathogen isolates.