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.

锈菌是对作物和生态系统造成负面影响的主要病原体。由具有新的毒力特征的菌株的出现驱动的最近的锈病流行需要对这些生物的进化机制有更好的了解。在这里，我们回顾了基因组规模分析的研究进展，以及对效应子候选基因进行功能验证的研究，这些候选基因已经有助于阐明导致毒力表型发生变化的过程。我们强调单倍型阶段基因组参考如何铺平道路，将这些过程与锈菌的生殖阶段联系起来，并为菌株之间的体细胞交换提供了证据，这是在无性种群中产生多样性的重要机制。随着数据可用性的提高，