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

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• 作者：Ji Eun Jeong ; Se Won Kang ; Hee-Ju Hwang ; So Young Park…
• 关键词：Pisidium (Neopisidium) coreanum ; Endemic species ; Expressed sequence tags ; Functional annotation ; Bone morphogenetic proteins
• 刊名：Genes & Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：37
• 期：12
• 页码：1041-1049
• 全文大小：599 KB
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• 作者单位：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)
  
  2. Department of Applied Biology, College of Natural Resources and Life Science, Dong-A University, 550-37 Nakdongdaero, Sahagu, Busan, 604-714, Korea
  1. Department of Life Science and Biotechnology, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 336-745, Korea
  3. School of Biotech Sciences, Trident Academy of Creative Technology, Bhubaneswar, Odisha, 751024, India
  4. National Institute of Biological Resources, Incheon, 404-170, Korea
  5. East Sea Fisheries Research Institute, National Fisheries Research and Development Institute (NFRDI), Gangneung, 210-861, Korea
  6. Korea Zoonosis Research Institute, Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do, 570-390, Korea
  7. Department of Biomedical Laboratory Science, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 336-745, Korea
  8. College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-Gu, Gwangju, 500-757, Korea
  9. Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Korea
  10. Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea
  
• 刊物主题：Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics; Human Genetics;
• 出版者：Springer Netherlands
• ISSN：2092-9293

文摘

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?) 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?0) 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