Domain gain or loss in fungal chitinases drives ecological specialization toward antagonism or immune suppression

The evolutionary origins of fungal effector proteins remain poorly understood, particularly how structural changes reprogram antimicrobial enzymes into host-adapted immune suppressors. Here, we show that domain modularity drives ecological specialization in chitinase effectors of the beneficial root endophyte Serendipita indica. The GH18 chitinase SiCHIT, which carries a C-terminal carbohydrate-binding module (CBM5), is expressed during fungal competition and antagonizes the fungal pathogen Bipolaris sorokiniana in the rhizosphere, thereby protecting plant roots. Deletion of the CBM5 abolishes this antifungal activity, while fusion of CBM5 to the CBM5-lacking paralog SiCHIT2 restores pathogen inhibition. In contrast, SiCHIT2 is induced during root colonization and suppresses chitin-triggered reactive oxygen species production, promoting immune evasion and host compatibility. These results identify CBM5 as a modular determinant of effector function, switching chitinase activity between microbial antagonism and host immune suppression. Our findings support an evolutionary scenario in which effector function in planta arises through domain loss and transcriptional divergence from an antimicrobial precursor, consistent with transitions along the saprotrophy-to-symbiosis continuum. Significance StatementEffector proteins play key roles in shaping fungal interactions with both plant hosts and microbial competitors, yet how these functions evolve remains unclear. Here, we show that structural domain modularity enables ecological specialization of two paralogous chitinases arising from gene duplication in the root endophyte Serendipita indica. Through domain deletion and fusion, we demonstrate that a carbohydrate-binding module (CBM5) determines whether a chitinase functions in microbial antagonism or immune evasion. Our findings provide mechanistic evidence for effector diversification via domain loss and transcriptional divergence, supporting an evolutionary trajectory from antimicrobial activity to host adaptation. This work advances our understanding of how modular architecture drives effector evolution and niche specialization in symbiotic fungi. HighlightsO_LIGain or loss of a CBM5 binding domain drives effector specialization between fungal antagonism and immune suppression C_LIO_LICBM5 acts as a modular determinant enabling antifungal activity in the GH18 chitinase SiCHIT C_LIO_LIThe CBM5-lacking paralog SiCHIT2 suppresses host immunity and promotes root colonization C_LIO_LIFunctional divergence following gene duplication illustrates evolutionary repurposing of an antimicrobial enzyme into an immune-suppressive effector C_LI