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Transcriptome profiling suggests roles of innate immunity and digestion metabolism in purplish Washington clam

  • Bo-Mi Kim
  • Do-Hwan Ahn
  • Hyejin Kim
  • Jung Sick Lee
  • Jae-Sung Rhee
  • Hyun Park
Research Article

Abstract

The purplish Washington clam (Saxidomus purpuratus) in the family Veneridae is distributed widely along the intertidal zones of northeast Asia and is increasingly being utilized as a commercially important food resource. Bivalves maintain homeostasis by regulating their food intake and digestion, innate immunity, and biotransformation in a mollusk-specific organ, the digestive gland. To understand digestive gland-specific pathways, we generated a high-quality de novo assembly of the digestive gland transcriptome of this clam using the Illumina Miseq platform. A total of 9.9 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 27,358 contigs with an N50 of 433 bp. Functional gene annotations were performed using Gene Ontology, Eukaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In the transcriptome, many crucial genes involved in innate immunity and digestion metabolism were detected. A number of enzymes associated with drug metabolism were annotated, as much as that identified from the whole transcriptome of the Pacific oyster Crassostrea gigas. We provide valuable sequence information of S. purpuratus to predict functional understandings of the bivalve-specific digestive gland. This resource will be valuable for researchers comparing gene compositions and their expression levels in the digestive glands of bivalves.

Keywords

Washington clam Saxidomus purpuratus Transcriptome Digestive gland Bivalve 

Notes

Acknowledgements

This work was supported by a grant, entitled “Polar genome 101 Project (PE18080)” funded by the Korea Polar Research Institute of South Korea and was also supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1A6A1A06015181).

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflicts of interest.

Ethical approval

All animal handling and experimental procedures were approved by the Animal Welfare Ethical Committee and Animal Experimental Ethics Committee of Korea Polar Research Institute (KOPRI, Incheon, South Korea).

Supplementary material

13258_2018_750_MOESM1_ESM.xlsx (4.2 mb)
Supplementary material 1 (XLSX 4263 KB)

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Copyright information

© The Genetics Society of Korea and Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Unit of Polar GenomicsKorea Polar Research InstituteIncheonSouth Korea
  2. 2.Department of Aqualife MedicineChonnam National UniversityYeosuSouth Korea
  3. 3.Department of Marine Science, College of Natural SciencesIncheon National UniversityIncheonSouth Korea
  4. 4.Research Institute of Basic SciencesIncheon National UniversityIncheonSouth Korea
  5. 5.Polar SciencesUniversity of Science & TechnologyDaejeonSouth Korea

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