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Development of DNA chip for verification of 25 microalgae collected from southern coastal region in Korea

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Abstract

Countless species occur in the marine microalgal domain. Some are used as health functional foods or medical products but many species are harmful such as those that cause the red tide. Therefore, it is necessary to conduct prompt and accurate identification of microalgal species. As it is quite difficult to accurately distinguish all species in terms of morphology, we performed DNA barcoding analysis using molecular markers for more accurate and rapid screening. DNA barcoding analysis, i.e., DNA chip technology, is a powerful method for studies on microalgal taxonomy and biodiversity. We used the mitochondrial cytochrome c oxidase subunit I (mtCOI) as a barcoding gene to identify microalgal species. In this study, the diversity and phylogenetic differences among different microalgae were analyzed. Additionally, a microalgal species-specific probe was screened by 21–23 bp and the result was printed on silylated slide for use in a robotic microarrayer. As a result, we performed a DNA chip assay for each of 25 microalgal species and determined that the COI barcode gene was suitable as a marker gene, as it could identify various microalgae from the Korean South Sea by species.

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References

  1. Kim, D. et al. Red to red-the marine bacterium Hahella chejuensis and its product prodigiosin for mitigation of harmful algal blooms. J. Microbiol. Biotechnol. 18, 1621–1629 (2008).

    CAS  Google Scholar 

  2. Hinder, S.L. et al. Toxic marine microalgae and shellfish poisoning in the British isles: history, review of epidemiology, and future implications. Environ. Health. 10, 54 (2011).

    Article  Google Scholar 

  3. Moretti, V., Turchini, G., Bellagamba, F. & Caprino, F. Traceability issues in fishery and aquaculture products. Vet. Res. Commun. 27, 497–505 (2003).

    Article  Google Scholar 

  4. Cunningham, E. & Meghen, C. Biological identification systems: genetic markers. Rev. Sci. Tech. 20, 491 (2001).

    CAS  Google Scholar 

  5. Ratnasingham, S., Hebert, P.D.N. & Gravenor, M.B., BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Notes. 7, 355–364 (2007).

    Article  CAS  Google Scholar 

  6. Yoon, H., Kim, G., Jeong, D., Jung, J. & Chung, I. Development of salmon identification DNA chip based on mitochondrial COIII-ND3-ND4L variations. Bio-Chip J. 2, 287–295 (2008).

    Google Scholar 

  7. Park, J.Y. et al. A DNA microarray for species identification of cetacean animals in Korean water. Bio-Chip J. 4, 197–203 (2010).

    CAS  Google Scholar 

  8. Kim, S. et al. DNA chip for species identification of Korean freshwater fish: A case study. BioChip J. 5, 72–77 (2011).

    Article  CAS  Google Scholar 

  9. Hebert, P.D.N., Ratnasingham, S. & de Waard, J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond., B, Biol. Sci. 270, S96 (2003).

    Article  CAS  Google Scholar 

  10. Robba, L., Russell, S.J., Barker, G.L. & Brodie, J. Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). Am. J. Bot. 93, 1101–1108 (2006).

    Article  CAS  Google Scholar 

  11. Alverson, A.J. & Kolnick, L. Intragenomic Nucleotide Polymorphism Among Small Subunit (18S) Rdna Paralogs in the Diatom Genus Skeletonema (Bacillariophyta) 1. J. Phycol. 41, 1248–1257 (2005).

    Article  CAS  Google Scholar 

  12. Moniz, M.B.J., Kaczmarska, I. & Gravenor, M.B. Barcoding diatoms: Is there a good marker? Mol. Ecol. Resour. 9, 65–74 (2009).

    Article  CAS  Google Scholar 

  13. Hebert, P.D. & Gregory, T.R. The promise of DNA barcoding for taxonomy. Syst. Biol. 54, 852–859 (2005).

    Article  Google Scholar 

  14. Hajibabaei, M., Singer, G.A., Clare, E.L. & Hebert, P.D. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biol. 5, 24 (2007).

    Article  Google Scholar 

  15. Hebert, P.D.N., Cywinska, A., Ball, S.L. & DeWaard, J.R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond., B, Biol. Sci. 270, 313 (2003).

    Article  CAS  Google Scholar 

  16. Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W. & Hebert, P.D. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. U S A 103, 968–971 (2006).

    Article  Google Scholar 

  17. Folmer, O., Black, M.A., Hoch, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).

    CAS  Google Scholar 

  18. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596 (2007).

    Article  CAS  Google Scholar 

  19. Engelmann, J.C. et al. Modelling cross hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Mol. Ecol. Resour. 9, 83–93 (2009).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656-830, Korea

    Gunsup Lee, Seungshic Yum, Seonock Woo & Taek-Kyun Lee

  2. Medical Research Center of Neural Dysfunction, Gyeonsang National University, Jinju, 660-751, Korea

    So Yun Park

  3. Marine Living Resources Research Department, Korea Institute of Ocean Science and Technology, Ansan, Gyeonggi-do, 425-600, Korea

    Youn-Ho Lee

  4. Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd., Sangnok-gu, Ansan, Gyeonggi-do, 426-791, Korea

    Seung Yong Hwang

  5. Korea South Pacific Ocean Research Center, Korea Institute of Ocean Science and Technology, Ansan, Gyeonggi-do, 425-600, Korea

    Heung-Sik Park

  6. Department of Genetic Engineering, Sungkyunkwan University, 300 Chunchun-dong, Jangan-gu, Suwon, 440-746, Korea

    Sang Hyun Moh & Sukchan Lee

Authors
  1. Gunsup Lee
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  2. So Yun Park
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  3. Seungshic Yum
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  4. Seonock Woo
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  5. Youn-Ho Lee
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  7. Heung-Sik Park
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  8. Sang Hyun Moh
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  9. Sukchan Lee
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  10. Taek-Kyun Lee
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Correspondence to Gunsup Lee.

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Lee, G., Park, S.Y., Yum, S. et al. Development of DNA chip for verification of 25 microalgae collected from southern coastal region in Korea. BioChip J 6, 325–334 (2012). https://doi.org/10.1007/s13206-012-6404-0

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  • DOI: https://doi.org/10.1007/s13206-012-6404-0

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