Comparative Proteomics Reveals Conserved and Lineage-Specific Molecular Toolkits in Lophotrochozoan Biomineralization

Animal biomineralization has evolved repeatedly, yielding diverse skeletal structures. A key question is whether this diversity stems from molecular convergence or a shared ancestral toolkit. Studying lophotrochozoans-a group with carbonate, phosphate, iron, and mixed mineralization systems-provides an ideal framework for addressing this issue but remains underrepresented in comparative omics studies. Here, we present a genome assembly and shell matrix proteome of the phosphate-biomineralizing brachiopod Lingula anatina CN, derived from a geographically distinct population. By integrating these data with comparative proteomic analysis across seven lophotrochozoan lineages representing diverse mineralization chemistries, we provide novel insights into the molecular basis of biomineralization. Sequence-based comparisons reveal extensive lineage specificity of shell matrix proteins, with little conservation across distant taxa. In contrast, domain-level analyses uncover a broadly conserved repertoire of functional modules-including EF-hand, von Willebrand factor type A, collagen-related, chitin-binding, and ferritin-like domains-recurrently recruited into shell matrix proteins across lineages. Importantly, similarity in shell matrix protein composition correlates more strongly with mineralization chemistry than with phylogenetic distance. Specifically, phosphate-mineralizing systems share a higher proportion of conserved shell matrix proteins and domains across deep evolutionary distances than do carbonate-based systems, indicating that mineral chemistry exerts a dominant selective pressure on the evolution of biomineralization-associated proteins. Lineage-specific innovations appear to arise primarily through domain shuffling, expansion of low-complexity regions, and gene family diversification. These findings support a model wherein lophotrochozoan biomineralization is underpinned by a shared ancestral molecular toolkit, differentially filtered and elaborated according to mineral chemistry, providing new insights into the early evolution of animal skeletal systems.