Bacterial domain fusion drives biomineralization innovation in Colepidae ciliates

Mineralized external structures have evolved independently across unicellular eukaryotes. Within the phylum Ciliophora , this trait’s restriction to the family Colepidae makes it an ideal model for dissecting the genomic basis of this innovation. Here, we assembled high-quality macronuclear genomes for three Colepidae species ( Coleps hirtus , Levicoleps biwae , and Coleps viridis ), and uncovered a marked expansion of gene families implicated in calcium carbonate biomineralization. Phylogenetic analysis reveals that a novel aldo-keto reductase ( Aldo ) domain was horizontally transferred from bacteria to the Colepidae lineage. This domain was incorporated into a novel fusion protein exclusive to Colepidae , where the N-terminal Aldo domain is fused to a canonical carbonic anhydrase ( Carb ) catalytic domain. RNA interference shows that Carb::Aldo is required for calcified armor and normal physiology. Together, these findings reveal a previously underappreciated evolutionary route to complex phenotypes in eukaryotes, mediated by bacterial domain fusion and gene-family expansion. This work highlights that subgene-scale horizontal gene transfer (HGT) from bacteria may be an overlooked mechanism driving the evolution of eukaryotic complexity. IMPORTANCE Biomineralization is a key ecological trait, yet its genomic basis in early-branching eukaryotes remains largely elusive. Here, we establish the ciliate family Colepidae as a tractable genomic model for studying calcium carbonate biomineralization. We reveal that the emergence of their calcified armor coincides with a massive expansion of biomineralization-related gene families and a highly unusual subgene-scale horizontal gene transfer from bacteria. We functionally validated that a novel fusion protein, which combines a co-opted bacterial domain with a eukaryotic catalytic domain, is strictly required for armor synthesis. This study not only illuminates the molecular machinery of ciliate biomineralization but also profoundly reshapes our understanding of evolutionary innovation, demonstrating how the hijacking and repurposing of bacterial genetic fragments can orchestrate complex structural adaptations in eukaryotes.