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Abstract -  Fungal diseases are among the most significant causes of wheat yield loss globally and pose a serious threat to food security. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is currently the most damaging wheat disease and is found on every continent where wheat is cultivated. Biocontrol agents – organisms that naturally antagonise plant pathogens – offer promising alternatives to conventional chemical controls. Among these, rust hyperparasitic fungi attack Pst urediniospores while they remain in pustules on wheat leaves, exploiting the spores’ rich nutrient stores.

My PhD research explored the genomic and transcriptomic underpinnings of this parasitic interaction. What began as a serendipitous discovery of a Penicillium coffeae isolate growing atop Pst pustules here at ANU led to a detailed investigation of its biology. Through comparative transcriptomic analysis during infection, I identified a suite of upregulated genes with an emphasis on cell wall-degrading enzymes, nutrient transporters, peroxiredoxins and secondary metabolite clusters, potentially involved in hyperparasitism. I selected 18 of those genes for CRISPR-Cas9 knockout. After extensive method optimisation, I developed a robust in vitro phenotyping system, using qPCR to quantify changes in mutant growth relative to the wild type. Expanding beyond Penicillium coffeae ANU01, I also isolated over 40 potential hyperparasites from rust-infected leaves around the ACT. Ten were selected for further study using genome assembly, annotation, and transcriptomics. This revealed both shared mechanisms and isolate-specific strategies used to parasitise rust spores. Finally, I used RNAseq data to explore the parasitic event from the perspective of Pst itself, uncovering a complex and coordinated response to parasitic attack.

Biography - Jack joined the Rathjen lab as an honours student in 2020, just as the COVID-19 lockdown began. He began his PhD in 2022, continuing his exploration of rust hyperparasitism, with a focus on Penicillium coffeae ANU01. His research combines molecular genetics, transcriptomics and bioinformatics to unravel the biology of fungal-fungal interactions.