Comprehensive pan-effectome investigation reveals central effector genes in woody plant pathogen Botryosphaeriaceae

Effectors are the relatively rapidly evolving genes in fungal phytopathogens. Elucidating the conservation and diversity of effectors is essential to understand the infection mechanisms of phytopathogens. Botryosphaeriaceae encompasses woody host pathogens causing significant economic loss worldwide. However, the pathogenicity mechanisms of these species remain poorly understood. In this study, we comparatively analyzed the effectomes of 25 Botryosphaeriaceae species to characterize the evolutionary dynamics of effector genes at the family level. We identified 56-183 candidate secreted effector proteins (CSEPs) across each of these species. Gene gain events occurred both before and after Botryosphaeriaceae diverged into different genera, while gene loss at the species level has played a prominent role in shaping the effector repertoire. Through pan-effectome analysis, conserved and diversified CSEP families were identified in Botryosphaeriaceae, with the number of conserved CSEP families significantly lower than that of diversified CSEP families. Horizontal gene transfer (HGT) analysis revealed that conserved CSEPs are likely inherited through vertical transmission, whereas many genes from the diversified CSEP families appear to have been acquired through HGT. Conserved CSEPs exhibit earlier expression onset and maintain longer expression duration compared to diversified CSEPs during host infection, and they can suppress plant immunity.IMPORTANCEOur results provide compelling evidence for the existence of conserved candidate secreted effector proteins (CSEPs) within the Botryosphaeriaceae family, which may play pivotal roles in woody plant infection. These findings not only deepen our understanding of effector evolution in fungal pathogens but also lay a foundational framework for developing targeted strategies to mitigate the impact of Botryosphaeriaceae-related diseases in woody crops.