Phenotypic convergence is widespread in nature, but the degree of genetic convergence between extremely divergent taxa, e.g. inter-phyla of Crustacea and Mollusca, is not yet clear. Barnacles are an ideal model with which to study this issue because they are a unique group of crustaceans that share phenotypes with more similarities with many molluscs, including calcareous shells, a sessile lifestyle and intertidal habitats. Herein, we report the chromosome-level genome assembly of a stalked barnacle, Capitulum mitella, and reveal a genome-wide strong convergent molecular evolution in barnacles and molluscs, including coexpansion of biomineralization and antistress genes and origination of lineage-specific orphan genes for their settlement. Some expanded gene families, e.g. lectin BRA and HSP70B2, are even only present in these two groups of organisms but not in their nonshell/non-intertidal relatives. Thus, barnacles adopt similar mechanisms to molluscs for shell formation, settlement and intertidal adaptation. However, unlike molluscs, barnacles have undergone whole-genome duplication for their adaptive evolution of intertidal sessile life and adopted different holdfast systems for settlement and novel organic matrixes for shell formation. Therefore, we suggest that selection pressures driving convergent evolution may strongly act in organisms inhabiting similar environments regardless of phylogenetic distance. The convergence signatures shed light on the origin of the shell and sessile lifestyle of barnacles and molluscs, while non-convergence signatures contribute to their morphological and functional specificities.

Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 42176105Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31830100Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 41876167