A key innovation in the evolution of calcareous sponges was the ability to form calcite spicules. Several genes involved in this process have been characterized in the model organism Sycon ciliatum. These genes are expressed in active sclerocytes during different stages of spicule formation and are, in some cases, specific to certain spicule types. Many lack clear orthologs in other sponge classes, suggesting they represent genetic innovations dating back to the last common ancestor of extant Calcarea.
Here, we investigate the evolution of key biomineralization genes in Calcarea using genomic, transcriptomic, and proteomic data from both major subclasses, Calcinea and Calcaronea. Our results reveal that several of these genes are orthologous within Calcarea and absent from other sponge lineages. These findings support the growing body of evidence that spicule formation evolved multiple times independently in different sponge classes. Within Calcarea, gene innovation followed by duplication and neofunctionalization has refined the biomineralization toolkit, giving rise to spicule-type-specific functions.