Evolutionary diversification and immunoprofiling of cathepsin L toolkit in common carp

Cysteine cathepsins are central regulators of lysosomal proteolysis, immune and metabolic homeostasis, yet the evolutionary forces shaping their diversification in vertebrates remain incompletely understood. Teleost fishes, particularly polyploid lineages, provide a powerful system to examine how whole-genome duplication remodels protease repertoires and regulatory networks. Here, using the polyploid common carp model, we identify nine cathepsin L (ctsl) paralogs retained after ancestral and lineage-specific whole-genome duplications, and show that these duplicates have undergone spatially distributed expression divergence. Paralog expression is strongly partitioned across tissues and immune compartments: ctsl.1A/B are enriched at mucosal barriers, whereas ctslaA/B predominate in metabolic and systemic immune hubs and are the only ctsl transcripts detected in circulating blood and head kidney leukocytes. Structural modelling predicts variation in protease loop architecture and active-site cleft geometry, suggesting divergent substrate preferences and/or catalytic properties. During infection with Sphaerospora molnari, a myxozoan pathogen, inflammatory cytokine induction is accompanied by transient ctsl downregulation, followed by a cell- and time-dependent reprogramming of proteolytic profiles as disease progresses. Collectively, these findings reveal a transcriptional pattern of ctsl regulation uncoupled from cytokine expression dynamics, emerging from retained ctsl duplicates. Moreover, they demonstrate how polyploidization can generate tissue- and cell-specific regulation of lysosomal pathways that balance host defense and homeostasis.