Stage‐specific transcriptome profiling highlights key modules associated with structurally conserved secreted proteins in <i>Puccinia polysora</i> infection of maize

Abstract Southern corn rust (SCR), caused by the biotrophic fungal pathogen Puccinia polysora , is a globally significant disease that poses a severe threat to maize production, particularly in tropical and subtropical regions. Despite its economic importance, many aspects of the molecular interactions between P. polysora and maize remain poorly understood. In this study, we performed stage‐specific transcriptome profiling to explore gene expression dynamics during key phases of P. polysora infection: conidia formation, spore germination, penetration, and colonization. We identified and characterized co‐regulated modules of effector proteins that are critical for successful host infection. Utilizing AlphaFold3, we identified structurally conserved proteins co‐expressed throughout the infection process. Notably, Cluster 7, a structurally conserved protein group, exhibited uniquely peak expression during the penetration stage, suggesting a pivotal role in overcoming host defenses. This research offers new insights into the molecular processes involved in P. polysora infection and provides a valuable resource for developing novel strategies to mitigate the global impact of SCR.