Strain-level diagnostics of fungal crop pathogens enabled by fully-phased isolate genomes

Fungal rust pathogens are a major threat to the global food supply chain. Oat crown rust canhave a devastating impact of oat production leading to losses as high as 35% in South Dakota and50% in Minnesota in 2014.Understanding their spread evolution and virulence requires a deeperlevel of genomic information than we currently possess.Despite current surveillance activities andample rust collections in various countries there has been a lag in the development of moleculardiagnostic tools. Pilot studies using the wheat stripe rust pathogen demonstrate ability to trace rustisolates to the lineage level and fail to provide strain-specific information.One of the mainchallenges in understanding many rust genomes is their complex (dikaryotic) nature where strainscontain genomic information from two independent nuclei. It has also been demonstrated that theevolution of virulence could be mediated by hybridization events between two rust strains (e.g.emergence of the wheat stem rust Ug99) adding to the complex genomic structure and presentingsignificant obstacle to genetic analysis and diagnostics.Using cutting edge genomic tools it is nowpossible and affordable to generate full chromosome-scale rust genomes and separate theirconstituent sub-genomes as was demonstrated by the wheat stem rust pathogen.We propose toapply this methodology to a set of diverse oat crown rust isolates in order to develop a referencelibrary of fully-phased chromosome-scale genomes that will be used as a foundation forsurveillance diagnostics and will enable the identification of novel virulence factors. The ability toleverage high-quality genomic information from sets of rust strains will transform our ability totrack their spread and understand the evolution of fungal virulence.