The modular origin and evolutionary expansion of the enigmatic DGF-1 protein family in trypanosomatids

Abstract

Large multigene families are a hallmark of trypanosomatid genomes and play major roles in genome plasticity and parasite adaptation. Among them, the Dispersed Gene Family 1 (DGF-1) of Trypanosoma cruzi remains one of the least understood because of its large size, repetitiveness, and fragmented annotations. Here, using a high-quality long-read assembly of T. cruzi, we performed comprehensive re-annotation and structural characterization of DGF-1. We identified seven tandemly repeated structural modules, here termed ribs, that form the extracellular region. This is followed by a distinct C-terminal membrane-associated region containing a conserved hat domain and multiple transmembrane helices. These domains are highly conserved across paralogous copies and the 7 ribs cluster according to positional identity rather than gene origin, indicating that the canonical seven-rib architecture predates the expansion of the family. DGF-1 proteins are present in the early-branching trypanosomatid species Paratrypanosoma confusum and several other trypanosomatids but absent in Leishmania and African trypanosomes, consistent with multiple independent secondary losses. Comparative analyses across Euglenozoa indicate that the DGF-1 architecture did not originate in free-living bodonids. Instead, Bodo saltans contains proteins with rib-like domains and others containing the membrane-associated region, whereas the first complete DGF-1 architecture appears in P. confusum. Phylogenetic and comparative genomic analyses indicate that the family subsequently underwent lineage-specific losses and independent expansions, the largest expansion occurring in T. cruzi. Together, these findings reconstruct the evolutionary emergence of the DGF-1 architecture from pre-existing structural modules and provide a framework for one of the largest and most enigmatic gene families in trypanosomatids.