Genes & Genomics

, Volume 38, Issue 4, pp 359–365 | Cite as

Transcriptome profiling of the Pacific oyster Crassostrea gigas by Illumina RNA-seq

  • Hyun-Jeong Lim
  • Jong-Sung Lim
  • Jeong-Soo Lee
  • Beom-Soon Choi
  • Dong-Inn Kim
  • Haeng-Woon Kim
  • Jae-Sung RheeEmail author
  • Ik-Young ChoiEmail author
Research Article


In this study, the whole transcriptome of the Pacific oyster Crassostrea gigas was sequenced using Illumina RNA-seq. De novo assembly was performed with 33,750,764 raw reads using Trinity, which assembled 87,887 contigs. Transdecoder found 41,542 candidate coding contigs which showed homology to other species by BLAST analysis. Functional gene annotation was performed by Gene Ontology and KEGG pathway analyses. Finally, we identified a number of expressed gene pathways for C. gigas representing a useful model animal for gene information-based study such as environmental monitoring, immune-relevant aquaculture, and ecotoxicogenomics studies to uncover molecular mechanisms of stress-triggered sensitivity and physiological response to C. gigas.


Oyster Crassostrea gigas Transcriptome RNA-seq 



This work was supported by a Grant (RP-2015-AG-089) funded to Hyun-Jeong Lim, National Institute of Fisheries Science of the Korean government.

Compliance of bioethical standard

All the experiments were approved by the animal care and use committee of National Fisheries Research and Development Institute (NFRDI, Pusan, South Korea).

Conflict of Interest

All authors claim no conflicts of interest.

Supplementary material

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Supplementary material 1 (DOCX 15 kb)
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Supplementary material 2 (PPTX 75 kb)
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Supplementary material 3 (XLSX 4999 kb)


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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2015

Authors and Affiliations

  • Hyun-Jeong Lim
    • 1
  • Jong-Sung Lim
    • 2
  • Jeong-Soo Lee
    • 2
  • Beom-Soon Choi
    • 2
  • Dong-Inn Kim
    • 2
  • Haeng-Woon Kim
    • 1
  • Jae-Sung Rhee
    • 3
    Email author
  • Ik-Young Choi
    • 2
    Email author
  1. 1.West Sea Fisheries Research InstituteNational Fisheries Research and Development InstituteIncheonSouth Korea
  2. 2.National Instrumentation Center for Environmental Management, College of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
  3. 3.Department of Marine Science, College of Natural SciencesIncheon National UniversityIncheonSouth Korea

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