Animal cells and systems

The Korean Society for Integrative Biology (한국통합생물학회)
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Korea Barcode of Life Database System (KBOL)

  • Kim, Sung-Min (Interdisciplinary Program in Bioinformatics, Seoul National University) ;
  • Kim, Chang-Bae (Department of Green Life Science, Sangmyung University) ;
  • Min, Gi-Sik (Department of Biological Sciences, Inha University) ;
  • Suh, Young-Bae (Natural Products Research Institute, Seoul National University) ;
  • Bhak, Jong (Theragen Bio Institute) ;
  • Woo, Tae-Ha (Omicsis Inc., Bio Venture Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Koo, Hye-Young (Department of Biological Science, Sangji University) ;
  • Choi, Jun-Kil (Department of Biological Science, Sangji University) ;
  • Shin, Mann-Kyoon (Department of Biological Sciences, University of Ulsan) ;
  • Jung, Jong-Woo (Department of Science Education, Ewha Womans University) ;
  • Song, Kyo-Hong (Wildlife Genetic Resources Center, National Institute of Biological Resources) ;
  • Ree, Han-Il (Department of Environmental Medical Biology, Institute of Tropical Medicine, and Korean National Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine) ;
  • Hwang, Ui-Wook (Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University) ;
  • Park, Yung-Chul (Department of Forest Environment Protection, College of Forest & Environmental Science, Kangwon National University) ;
  • Eo, Hae-Seok (Future IT R&D Laboratory, LGE Advanced Research Institute) ;
  • Kim, Joo-Pil (Joopil Spider Museum) ;
  • Yoon, Seong-Myeong (Department of Biology Education, Chosun University) ;
  • Rho, Hyun-Soo (East Sea Research Institute, Korea Ocean Research & Development Institute) ;
  • Kim, Sa-Heung (Marine Biodiversity Research institute, IN THE SEA Korea Co., Ltd.) ;
  • Lee, Hang (Conservation Genome Resource Bank for Korean Wildlife and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University) ;
  • Min, Mi-Sook (Conservation Genome Resource Bank for Korean Wildlife and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University)
  • Received : 2011.03.10
  • Accepted : 2011.05.29
  • Published : 2012.02.28
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Abstract

A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using short DNA sequences provides an effective molecular tool for species identification. We constructed a large-scale database system that holds a collection of 5531 barcode sequences from 2429 Korean species. The Korea Barcode of Life database (KBOL, http://koreabarcode.org) is a web-based database system that is used for compiling a high volume of DNA barcode data and identifying unknown biological specimens. With the KBOL system, users can not only link DNA barcodes and biological information but can also undertake conservation activities, including environmental management, monitoring, and detecting significant organisms.

Keywords

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  2. Bensasson D, Zhang DX, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol. 16(6):314321. https://doi.org/10.1016/S0169-5347(01)02151-6
  3. Benson DA, Karsch-Mizrachi IK, Lipman DJ, Ostell J, Wheeler DL.2008. GenBank. Nucleic Acids Res. 36 Suppl1:D25-D30.
  4. Core D.2004. Darwin Core Schema (version 1.3), a draft standard of the Taxonomic Database Working Group (TDWG).
  5. Dasmahapatra KK, Mallet J. 2006. Taxonomy: DNA barcodes: recent successes and future prospects. Heredity. 97(4):254-255. https://doi.org/10.1038/sj.hdy.6800858
  6. Eddy SR. 1998. Profile hidden Markov models. Bioinformatics. 14(9):755-763. https://doi.org/10.1093/bioinformatics/14.9.755
  7. Hajibabaei M, Dewaard JR, Ivanova NV, Ratnasingham S, Dooh RT, Kirk SL, Mackie PM, Hebert PDN. 2005. Critical factors for assembling a high volume of DNA barcodes. Phil Trans R Soc B. 360(1462):1959-1967. https://doi.org/10.1098/rstb.2005.1727
  8. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. TIG. 23(4):167-172. https://doi.org/10.1016/j.tig.2007.02.001
  9. Hebert PDN, Gregory TR. 2005. The promise of DNA barcoding for taxonomy. Syst Biol. 54(5):852-859. https://doi.org/10.1080/10635150500354886
  10. Hebert PDN, Ratnasingham S, de Waard JR.2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B. 270 Suppl1:S96-S99. https://doi.org/10.1098/rsbl.2003.0025
  11. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 235(5):1501-1531. https://doi.org/10.1006/jmbi.1994.1104
  12. Kim S, Eo HS, Koo H, Choi JK, Kim W. 2010. DNA barcode-based molecular identification system for fish species. Mol Cells. 30(6):507-512. https://doi.org/10.1007/s10059-010-0148-2
  13. Lim J, Kim SY, Kim S, Eo HS, Kim CB, Paek WK, Kim W, Bhak J. 2009. BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources. BMC Genomics. 10 Suppl 3:S8.
  14. Markmann M, Tautz D. 2005. Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Phil Trans R Soc B. 360(1462):1917-1924. https://doi.org/10.1098/rstb.2005.1723
  15. Park HC, Lee YM, Choi WY.2008. A study on technical development of DNA barcoding analyses. Anim Cells Syst. 12 Suppl:G601-G700.
  16. Pfenninger M, Nowak C, Kley C, Steinke D, Streit B. 2007. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Mol Ecol. 16(9):1957-1968. https://doi.org/10.1111/j.1365-294X.2006.03136.x
  17. Radulovici AE, Archambault P, Dufresne F. 2010. DNA Barcodes for marine biodiversity: moving fast forward? Diversity. 2(4):450-472. https://doi.org/10.3390/d2040450
  18. Ratnasingham S, Hebert PDN. 2007. BOLD: the Barcode of Life Data System (http://www. barcodinglife. org). Mol Ecol Notes. 7(3):355-364. https://doi.org/10.1111/j.1471-8286.2007.01678.x
  19. Rubinoff D. 2006. Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol. 20(4):1026-1033. https://doi.org/10.1111/j.1523-1739.2006.00372.x
  20. Song H, Buhay JE, Whiting MF, Crandall KA. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. PNAS. 105(36):13486-13491. https://doi.org/10.1073/pnas.0803076105
  21. Zmasek CM, Eddy SR. 2001. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics. 17(4):383-384. https://doi.org/10.1093/bioinformatics/17.4.383