Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum

The wheat pathogen Parastagonospora nodorum has emerged as a model necrotrophic fungal species with growing genomic resources. Recent population-level pan-genome studies were leveraged to provide novel insights into pathogen evolution and effector-like gene contents relevant to local crop disease outbreaks. In this study, we examined 156 isolates representing a regional population from the Western Australian (WA) wheat-belt region, and 17 internationally sourced isolates. We observed a highly diverse local population, within which were numerous small and highly similar clusters of isolates from hotter and drier regions. Pan-genome assembly and orthologous gene datasets resulted in 3579 predicted effector candidates, 2291 of which exhibited presence-absence variation (PAV) across the population, and 1362 were specific to WA isolates. There was an abundance of mutations (including repeat-induced point mutation (RIP)), distributed in hot-spots within the pan-genomic landscape that were rich in effector candidates. Three characterised effector loci (ToxA, Tox1 and Tox3) were located within sub- telomeric regions of lower diversity, but were nestled within larger high-diversity regions. RIP was widespread across the genome, but non-synonymous RIP-like mutations were strongly selected against. These improved bioinformatic resources for P. nodorum, represent progressive advancements in fungal pan-genomics, with a view towards supporting region- specific surveillance of host-pathogen interactions.