Genes & Genomics

, Volume 37, Issue 12, pp 1041–1049 | Cite as

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

  • Ji Eun Jeong
  • Se Won Kang
  • Hee-Ju Hwang
  • So Young Park
  • Bharat Bhusan Patnaik
  • Changmu Kim
  • Soonok Kim
  • Myung-Mo Nam
  • Jae Bong Lee
  • Tae Hun Wang
  • Eun Bi Park
  • Sun Shin Yi
  • Yeon Soo Han
  • Jun-Sang Lee
  • Hong Seog Park
  • Yong Seok Lee
Research Article

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.

Keywords

Pisidium (Neopisidium) coreanum Endemic species Expressed sequence tags Functional annotation Bone morphogenetic proteins 

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Copyright information

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

Authors and Affiliations

  • Ji Eun Jeong
    • 2
  • Se Won Kang
    • 1
  • Hee-Ju Hwang
    • 1
  • So Young Park
    • 1
  • Bharat Bhusan Patnaik
    • 1
    • 3
  • Changmu Kim
    • 4
  • Soonok Kim
    • 4
  • Myung-Mo Nam
    • 5
  • Jae Bong Lee
    • 6
  • Tae Hun Wang
    • 1
  • Eun Bi Park
    • 1
  • Sun Shin Yi
    • 7
  • Yeon Soo Han
    • 8
  • Jun-Sang Lee
    • 9
  • Hong Seog Park
    • 10
  • Yong Seok Lee
    • 1
  1. 1.Department of Life Science and BiotechnologySoonchunhyang UniversityAsanKorea
  2. 2.Department of Applied Biology, College of Natural Resources and Life ScienceDong-A UniversityBusanKorea
  3. 3.School of Biotech SciencesTrident Academy of Creative TechnologyBhubaneswarIndia
  4. 4.National Institute of Biological ResourcesIncheonKorea
  5. 5.East Sea Fisheries Research InstituteNational Fisheries Research and Development Institute (NFRDI)GangneungKorea
  6. 6.Korea Zoonosis Research InstituteChonbuk National UniversityIksanKorea
  7. 7.Department of Biomedical Laboratory ScienceSoonchunhyang UniversityAsanKorea
  8. 8.College of Agriculture and Life ScienceChonnam National UniversityGwangjuKorea
  9. 9.Institute of Environmental ResearchKangwon National UniversityChuncheon-siKorea
  10. 10.Research Institute, GnC BIO Co., LTD.DaejeonRepublic of Korea

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