Butter clam genome assembly and analysis reveals the historical
adaptation of shellfish genome to changes in the marine environment
Abstract
Purple butter clam (Saxidomus purpuratus) is an economically important
bivalve shellfish. This species belongs to the subclass Heterodonta that
diverged in calcite seas with low magnesium concentrations. We sequenced
and assembled its genome and performed an evolutionary comparative
analysis. A total of 911 Mb assembly of S. purpuratus was anchored into
19 chromosomes and a total of 48,090 protein-coding genes were
predicted. We identified its repeat-based expanded genes that are
associated with the sodium/potassium-exchange ATPase complex. In
addition, different types of ion transporters were enriched in the
common ancestor of Heterodonta (calcium, sulfate, and lipid
transporters) and the specific evolution of S. purpuratus (calcium and
sodium transporters). These differences seem to be related to the
divergence times of Heterodonta (calcitic sea) and Veneraidea
(aragonitic sea). Furthermore, we analyzed the evolution of scavenger
receptor (SR) proteins in S. purpuratus, which are involved in a wide
range of immune responses, and compared them to the closely related
Cyclina sinensis. We showed that a small number of SR proteins,
exhibited collinearity between the two genomes, which is indicative of
independent gene evolution. Our genomic study provides an evolutionary
perspective on the genetic diversity of bivalves and their adaptation to
historical changes in the marine environment.