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Butter clam genome assembly and analysis reveals the historical adaptation of shellfish genome to changes in the marine environment
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  • Jungeun Kim,
  • Hui-Su Kim,
  • Jae-Pil Choi,
  • Min Sun Kim,
  • Seonock Woo,
  • Yeonghye Kim,
  • Yejin Jo,
  • Seungshic Yum,
  • Jong Bhak
Jungeun Kim
Personal Genomics Institute (PGI), Genome Research Foundation
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Hui-Su Kim
Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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Jae-Pil Choi
Personal Genomics Institute (PGI), Genome Research Foundation
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Min Sun Kim
Personal Genomics Institute (PGI), Genome Research Foundation
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Seonock Woo
Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan 49111, Republic of Korea.
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Yeonghye Kim
Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
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Yejin Jo
South Sea Environment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, Republic of Korea.
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Seungshic Yum
South Sea Environment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, Republic of Korea.
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Jong Bhak
Ulsan National Institute of Science and Technology (UNIST)
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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.

Peer review status:UNDER REVIEW

10 Mar 2021Submitted to Molecular Ecology Resources
26 Jul 2021Assigned to Editor
26 Jul 2021Submission Checks Completed
09 Aug 2021Reviewer(s) Assigned