ZymoR: Bridging plant pathology and automated bioinformatics for fungicide resistance profiling in Zymoseptoria tritici.

Abstract

Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), is one of the most destructive fungal pathogens of wheat worldwide. The extensive use of fungicides has driven the emergence of diverse resistance mechanisms involving multiple target-site genes, as well as non-target-site resistance. High-throughput sequencing (HTS) technologies now enable large-scale detection of resistance-associated genetic variation, yet routine implementation of HTS-based monitoring remains constrained by the lack of standardized analytical workflows and tools that translate sequence data into biologically meaningful resistance information. Here, we present ZymoR, a dedicated bioinformatics platform for automated molecular surveillance of fungicide resistance in Z. tritici. ZymoR integrates sequence quality assessment, mutation detection and CYP51 haplotype classification within a single user-friendly workflow. The platform incorporates a curated and expandable database of resistance-associated variants across the principal fungicide target genes, enabling standardized annotation of known resistance markers while facilitating the identification of previously undescribed variants. Unlike conventional variant-calling pipelines, ZymoR links detected genetic variation to standardized nomenclature and resistance-associated metadata, substantially reducing the bioinformatic expertise required for data interpretation. The ZymoR package was made available as an open-source tool via GitHub at https://github.com/Mordziarz/ZymoR .