The centriole and basal body (CBB) structure nucleates cilia and flagella, and 
is an essential component of the centrosome, underlying eukaryotic 
microtubule-based motility, cell division and polarity. In recent years, 
components of the CBB-assembly machinery have been identified, but little is 
known about their regulation and evolution. Given the diversity of cellular 
contexts encountered in eukaryotes, but the remarkable conservation of CBB 
morphology, we asked whether general mechanistic principles could explain CBB 
assembly. We analysed the distribution of each component of the human 
CBB-assembly machinery across eukaryotes as a strategy to generate testable 
hypotheses. We found an evolutionarily cohesive and ancestral module, which we 
term UNIMOD and is defined by three components (SAS6, SAS4/CPAP and 
BLD10/CEP135), that correlates with the occurrence of CBBs. Unexpectedly, other 
players (SAK/PLK4, SPD2/CEP192 and CP110) emerged in a taxon-specific manner. We 
report that gene duplication plays an important role in the evolution of CBB 
components and show that, in the case of BLD10/CEP135, this is a source of 
tissue specificity in CBB and flagella biogenesis. Moreover, we observe extreme 
protein divergence amongst CBB components and show experimentally that there is 
loss of cross-species complementation among SAK/PLK4 family members, suggesting 
species-specific adaptations in CBB assembly. We propose that the UNIMOD theory 
explains the conservation of CBB architecture and that taxon- and 
tissue-specific molecular innovations, gained through emergence, duplication and 
divergence, play important roles in coordinating CBB biogenesis and function in 
different cellular contexts.