Evolution of virulence in rust fungi — multiple solutions to one problem

[Display omitted] •Molecular basis of rust virulence follows the classic gene-for-gene concept.•Knockout mutations and amino acid sequence variation of effectors enable evolution.•Prevalence of sexual and asexual reproduction impacts on virulence diversity.•Genomic advances have recently allowed phasing of dikaryotic rust genomes.•Somatic hybridization can allow exchange of whole nuclei between strains. Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.