A conserved minimal core and modular extensions make the fungal flagellum

Flagellated fungi are pivotal for understanding the evolution of eukaryotic motility, yet knowledge of their flagellar proteins remains fragmentary. We assembled a cross-phyla atlas by mapping 303 reference flagellar proteins on 184 fungal proteomes. Out of 303 orthogroups, 231 orthogroups have fungal homologs, of which 128 orthogroups are specific to flagellated fungi. From these, we propose a 97-orthogroup minimal flagellum encompassing proteins shared by flagellated fungi. This minimal toolkit retains the axonemal core (tubulins, dynein arms), beat regulators (nexin–dynein regulatory complex, radial spokes), and essential intraflagellar transport (core IFT-B with key IFT-A and kinesin-2), plus a pared foundation for basal-body duplication and targeted trafficking (exocyst/TRAPP). Fungal lineages differ in the composition of flagellar modules. Neocallimastigomycota stand out as the most diverged among flagellated lineages with the broadest flagellar toolkit, including a complete BBSome, yet exhibit reductions in centriole-associated modules. Finally, we annotate two Pfam domains of unknown function DUF4470 & DUF4471 within DNAAF3 protein as a single Rossmann-like fold. We delineate a lean, conserved engine for fungal motility and a modular, lineage-specific layer that broadens regulation and sensory capacity. The conservation of flagellar proteins between fungi and animals opens up possibilities of experimental functional validation in models simpler than animals.