Neo-functionalization and co-option of Pif genes facilitate the evolution of a novel shell microstructure in oysters

Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unknown. Here, we present the first chromosome-level genome and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently evolved and co-opted genes as well as lineage-specific domains are involved in the formation of chalky layer in the oysters. Rapid mineralization involving chalky calcite are essential for reconstruction of the shell. Importantly, von Willebrand factor type A and chitin-binding domains are identified as basic members of molluscan biomineralization toolkit. We show that the well-known Pif shared a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky layer formation in oysters through a combination of gene duplication and domain reorganization. Our findings highlight neo-functionalization as a crucial mechanism for shell diversity, which may be applied more widely for studies on the evolution of metazoan biomineralization. This study also has potential implications for material science and biomimetic research.