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Expressed sequence tag analysis and annotation of genetic information from the freshwater clam, Pisidium (Neopisidium) coreanum endemic to Korea

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Abstract

Pisidium (Neopisidium) coreanum is a freshwater clam endemic to Korea. It has been classified as a vulnerable bivalve by the Korean Red List of threatened species and there exist no regional conservation measures. In the present study, we made an attempt to study the expressed sequence tags (ESTs) from the clam species for elucidating genomic information through the annotation of essential genes. A high-quality cDNA library was constructed from the whole body tissue of Pisidium coreanum yielding a collection of 5760 clones. The sequencing of the resultant clones identified 5656 ESTs assembled into 1312 non-redundant sequences, comprising of 791 contigs and 521 singletons. We identified 3265 and 3314 EST sequences showing significant matches (E value <1e−5) to known sequences in the mollusks sequence database (Malacological Society of Korea) and the NCBI non-redundant database, respectively. A total of 1674 putative sequences showed significant matches (E value of 1e−10) with the National Centre for Biotechnology Information-Eukaryotic Clusters of Orthologous Groups (NCBI KOG) database. These sequences were successfully assigned to classified biological processes including translation, ribosomal structure and biogenesis (18.61 %), post-translational modification, protein turnover and chaperones (13.29 %), energy production and conversion (13.86 %), cytoskeleton (12.78 %), and signal transduction mechanisms (7.15 %). Furthermore, we identified 16 transcripts showing high homology with bone morphogenetic protein 2-B that could pave an advancement towards bone therapeutics development.

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Acknowledgments

This work was supported by Soonchunhyang University Research Funding (20130600) and the Grant entitled “The Genetic and Genomic Evaluation of Indigenous Biological Resources” funded by the National Institute of Biological Resources (NIBR201503202).

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Authors and Affiliations

  1. Department of Life Science and Biotechnology, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 336-745, Korea

    Se Won Kang, Hee-Ju Hwang, So Young Park, Bharat Bhusan Patnaik, Tae Hun Wang, Eun Bi Park & Yong Seok Lee

  2. Department of Applied Biology, College of Natural Resources and Life Science, Dong-A University, 550-37 Nakdongdaero, Sahagu, Busan, 604-714, Korea

    Ji Eun Jeong

  3. School of Biotech Sciences, Trident Academy of Creative Technology, Bhubaneswar, Odisha, 751024, India

    Bharat Bhusan Patnaik

  4. National Institute of Biological Resources, Incheon, 404-170, Korea

    Changmu Kim & Soonok Kim

  5. East Sea Fisheries Research Institute, National Fisheries Research and Development Institute (NFRDI), Gangneung, 210-861, Korea

    Myung-Mo Nam

  6. Korea Zoonosis Research Institute, Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do, 570-390, Korea

    Jae Bong Lee

  7. Department of Biomedical Laboratory Science, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 336-745, Korea

    Sun Shin Yi

  8. College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-Gu, Gwangju, 500-757, Korea

    Yeon Soo Han

  9. Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Korea

    Jun-Sang Lee

  10. Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea

    Hong Seog Park

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  1. Ji Eun Jeong
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  2. Se Won Kang
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  14. Jun-Sang Lee
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Correspondence to Yong Seok Lee.

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This work was conducted in compliance with ethical standards. The sampling for experiments was conducted in accordance with the International Guiding Principles for Biomedical Research involving animals (1985) (http://www.ncbi.nlm.nih.gov/books/NBK25438/).

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Jeong, J.E., Kang, S.W., Hwang, HJ. et al. Expressed sequence tag analysis and annotation of genetic information from the freshwater clam, Pisidium (Neopisidium) coreanum endemic to Korea. Genes Genom 37, 1041–1049 (2015). https://doi.org/10.1007/s13258-015-0345-7

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