Hidden RIP mutation – a ‘back-seat driver’ of effector diversity revealed by pan-genome analysis of the necrotroph Parastagonospora nodorum across the Western Australian wheat-belt region.

Abstract The fungal species Parastagonospora nodorum is an important pathogen of wheat and model necrotroph with significant genomic resources. In this study, population-level pan-genome data for 173 P. nodorum isolates - 156 from the Western Australian (WA) wheat-belt, and 17 internationally-sourced isolates – were examined for genomic diversity and pathogenicity effector gene content. A heterothallic core population was observed across all regions of WA, with asexually-reproducing clonal clusters in dryer northern regions. An abundant potential for SNP diversity –the majority in the form of repeat-induced point (RIP)-like C-T transitions - was evenly spread across the genome, however increases in non-synonymous mutations were concentrated around repeat-rich regions. Known effector genes and effector-like candidates were typically located around these and sub-telomeric regions. Protein isoform profiles of known effector loci (SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5) indicated similarly low-level non-synonymous and high-level silent RIP-like mutations, and showed distinctive profiles across WA relative to international isolates. Prediction of novel effector genes across resulted in 186 candidate secreted predicted effector proteins (CSEPs), 69 with functional annotations that included 6 confirmed effectors. These new P. nodorum pan-genomic resources and diagnostic methods will support new approaches to region-specific surveillance and management of host-pathogen interactions in commercial crops.