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Identification of transposable elements fused in the exonic region of the olive flounder genome

Genes & Genomics volume 40, pages 707–713 (2018)Cite this article

Abstract

Transposable elements (TEs) are mobile genetic sequences that comprise a large portion of vertebrate genomes. The olive flounder (Paralichthys olivaceus) is a valuable marine resource in East Asia. The scope of most genomic studies on the olive flounder is limited to its immunology as their focus is the prevention of mass mortality of this species. Thus, for a broader understanding of the species, its genomic information is consistently in demand. Transcripts sequences were acquired from transcriptome analysis using gill tissues of 12 olive flounders. Distribution of TEs inserted in exonic region of the olive flounder genome was analyzed using RepeatMasker (http://www.repeatmasker.org/). We found 1140 TEs in the exonic region of the genome and long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) insertions occurred with forward orientation preferences. Transposons belonging to the hAt, Gypsy, and LINE 1 (L1) subfamilies were the most abundant DNA transposons, LTRs, and long interspersed elements (LINEs), respectively. Finally, we carried out a gene ontology analysis to determine the function of TE-fused genes. These results provide some genomic information about TEs that is useful for future research on changes in properties and functions of genes by TEs in the olive flounder genome.

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Acknowledgements

This research was a part of the project titled “Omics based on fishery disease control technology development and industrialization (20150242),” funded by the Ministry of Oceans and Fisheries, Korea.

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Authors and Affiliations

  1. Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea

    Gyu-Hwi Nam, Jeong-An Gim, Anshuman Mishra & Heui-Soo Kim

  2. Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea

    Gyu-Hwi Nam, Jeong-An Gim & Heui-Soo Kim

  3. Institute of Basic Science, Pukyong National University, Busan, 48513, Republic of Korea

    Anshuman Mishra

  4. Theragen Etex Bio Institute, Theragen Etex, Suwon, 16229, Republic of Korea

    Kung Ahn

  5. Department of Chemistry, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea

    Suhkmann Kim

  6. Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, Republic of Korea

    Do-Hyung Kim

  7. Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, 49267, Republic of Korea

    Hee-Jae Cha

  8. Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan, 47227, Republic of Korea

    Yung Hyun Choi

  9. Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong, Republic of Korea

    Chan-Il Park

  10. Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea

    Heui-Soo Kim

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  1. Gyu-Hwi Nam
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Correspondence to Heui-Soo Kim.

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Conflict of interest

Gyu-Hwi Nam declares that he has no conflict of interest. Jeong-An Gim declares that he has no conflict of interest. Anshuman Mishra declares that he has no conflict of interest. Kung Ahn declares that he has no conflict of interest. Suhkmann Kim declares that he has no conflict of interest. Do-Hyung Kim declares that he has no conflict of interest. Hee-Jae Cha declares that he has no conflict of interest. Yung Hyun Choi declares that he has no conflict of interest. Chan-Il Park declares that he has no conflict of interest. Heui-Soo Kim declares that he has no conflict of interest

Ethical approval

All experiments with the olive flounders in this study were carried out in accordance with the guidelines and regulation approved by Ethical Committee of Pukyong National University.

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Nam, GH., Gim, JA., Mishra, A. et al. Identification of transposable elements fused in the exonic region of the olive flounder genome. Genes Genom 40, 707–713 (2018). https://doi.org/10.1007/s13258-018-0676-2

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  • DOI: https://doi.org/10.1007/s13258-018-0676-2

Keywords

  • Paralichthys olivaceus
  • Transcriptome analysis
  • Bioinformatics
  • Transposable elements
  • TE-fused genes