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Analysis of genetic divergence according to each mitochondrial DNA region of Haliotis discus hannai

북방전복 (Haliotis discus hannai) 의 mitochondrial DNA 영역별 유전적 변이성 분석

  • 박철지 (국립수산과학원 육종연구센터) ;
  • 남원식 (국립수산과학원 육종연구센터) ;
  • 이정호 (국립수산과학원 육종연구센터) ;
  • 노재구 (국립수산과학원 육종연구센터) ;
  • 김현철 (국립수산과학원 육종연구센터) ;
  • 박종원 (국립수산과학원 육종연구센터) ;
  • 황인준 (국립수산과학원 육종연구센터) ;
  • 김성연 (국립수산과학원 육종연구센터)
  • Received : 2013.12.02
  • Accepted : 2013.12.24
  • Published : 2013.12.31

Abstract

The seven mitochondrial DNA regions (ND2, ND5, ND4, ND4L, ND6, ND1 and 12SrRNA) of Haliotis discus hannai were examined to estimate the availability as a genetic marker for the study of population genetic. The region with the highest genetic variation was ND4 (Haplotype diversity = 1.0000, Nucleotide diversity = 0.0108). On the other hand, ND2 and ND1 regions have significantly appeared genetic divergence between clusters (divergence of 90% and 87%). Also, pairwise $F_{ST}$ between clusters within ND2 and ND1 regions showed high values; 0.4061 (P = 0.0000), 0.4805 (P = 0.0000) respectively. Therefore we can infer that it is the most efficient and accurate way to analyze the region of ND4 with the highest variation in addition to the regions of ND2 and ND1, which formed clusters with high bootstrap value, for study of population genetic structure in this species.

본 연구는 우리나라의 주요양식 품종인 북방전복을 대상으로 지금까지 전복류에서는 사용되지 않았던 mtDNA의 protein coding 영역 ND2, ND5, ND4, ND4L, ND6, ND1의 6개영역과 protein noncoding 영역인 12SrRNA(ribosomal RNA) 을 포함해 총 7개 영역을 이용하여 각 영역의 유전적 변이성 및 개체간 유전적 유연관계 등을 분석하여 각 영역별 특성을 파악하고 이러한 특성을 고려하여 유전학적 분석에 적합한 분자유전마커를 개발하였다. 유전적 변이성은 ND4 영역 (Haplotype diversity = 1.000, Nucleotide diversity = 0.010823) 이 가장 높게 나타났으며, 개체간의 유전적 차이는 ND2 및 ND1 영역이 각각 90% 및 87%로 유의적으로 명확히 구분할 수 있었다. 따라서 유전적 변이성이 가장 높은 ND4 영역과 영역내의 클러스터 간의 유전적 차이가 명확한 ND2 및 ND1 영역을 복합적으로 활용할 경우 북방 전복의 집단유전학 및 계통분류학 분석에 유용한 분자유전마커로 사용할 수 있을 것이라 생각된다.

Keywords

References

  1. Ben, T.M., Lyndal J.K., Joanne M.M., Eliza S.J. and Peter J.H. (2005) Mitochondrial DNA Sequence and Gene Organization in the Australian Blacklip Abalone Haliotis rubra (Leach). Marine Biotechnology, 7: 645-658. https://doi.org/10.1007/s10126-005-0013-z
  2. Brown, W.M., George, M.J.R. and Wilson, A.C. (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America, 76: 1967-1971. https://doi.org/10.1073/pnas.76.4.1967
  3. Brykov, V.A., Polyakova, N., Skurikhina, L.A. and Kukleysky, A.D. (1996) Geographical and temporal mitochondrial DNA variability in populations of pink salmon. Journal of Fish Biology, 48: 899-909 https://doi.org/10.1111/j.1095-8649.1996.tb01485.x
  4. Conod, N., Bartlett, J.P., Evans, B.S. and Elliott, N.G. (2002) Comparison of mitochondrial and nuclear DNA analyses of population structure in the blacklip abalone Haliotis rubra Leach. Marine and Freshwater Research, 53: 711-718. https://doi.org/10.1071/MF01197
  5. Degnan, S.A., Imron, Geiger D.L. and Degnan, B.M. (2006) Evolution in temperate and tropical seas: disparate patterns in southern hemisphere abalone (Mollusca: Vetigastropoda: Haliotidae). Molecular Phylogenetics and Evolution, 41: 249-256. https://doi.org/10.1016/j.ympev.2006.06.023
  6. Duran, S., Palacin, C., Becerro, M.A., Turon, X. and Giribet, G. (2004) Genetic diversity and population structure of the commercially harvested sea urchin Paracentrotus lividus (Echinodermata, Echinoidea). Molecular Ecology, 13: 3317-3328. https://doi.org/10.1111/j.1365-294X.2004.02338.x
  7. Elliott, N.G., Bartlett, J., Evans, B. and Sweijd, N.A. (2002) Identification of Southern Hemisphere abalone (Haliotis) species by PCR-RFLP analysis of mitochondrial DNA. Journal of Shellfish Research, 21: 219-226.
  8. Estes, J.A., Lindberg, D.R. and Wray, C. (2005) Evolution of large body size in abalones (Haliotis) : patterns and implications. Paleobiology, 31: 591-606. https://doi.org/10.1666/04059.1
  9. Excoffier, L., Laval, G. and Schneider, S. (2006) Arlequin ver 3.11: An integrated software package for population genetics data analysis Computational and Molecular Population Genetics Lab (CMPG), Institute of Zoology University of Berne, Switzerland.
  10. Gruenthal, K.M. and Burton, R.S. (2008) Genetic structure of natural populations of the California black abalone (Haliotis cracherodii Leach, 1814), a candidate for endangered species status. Journal of Experimental Marine Biology and Ecology, 355: 47-58. https://doi.org/10.1016/j.jembe.2007.11.013
  11. Hamm, D.E. and Burton, R.S. (2000) Population genetics of black abalone, Haliotis cracherodii, along the central California coast. Journal of Experimental Marine Biology and Ecology, 254: 235-247. https://doi.org/10.1016/S0022-0981(00)00283-5
  12. Imron, Jeffrey, B., Hale, P., Degnan, B.M. and Degnan, S.M. (2007) Pleistocene isolation and recent gene flow in Haliotis asinina, an Indo-Pacific vetigastropod with limited dispersal capacity. Molecular Ecology, 16: 289-304.
  13. Kamarudin, K.R., Hashim, R. and Usup, G. (2010) Phylogeny of sea cucumber (Echinodermata: Holothuroidea) as inferred from 16S mitochondrial rRNA gene sequences. Sains Malaysiana, 39(2): 209-218.
  14. KNSO (2013) KOSIS Statistical DB. Korea National Statistical Office, Daefeon, Korea
  15. Lansman, R., Shade, R.O., Shapira, F. and Avise, J.C., (1981) The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. Journal of Molecular Evolution, 17: 214-226. https://doi.org/10.1007/BF01732759
  16. Lee, Y.H. (2003) Molecular pylogenies and divergence times of sea urchin species of Strongylocentrotidae, Echinoida. Molecular Biology and Evolution, 20: 1211-1221. https://doi.org/10.1093/molbev/msg125
  17. Lessios, H.A., Kane, J. and Robertson, D.R. (2003) Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans. Evolution, 57: 2026-2036. https://doi.org/10.1111/j.0014-3820.2003.tb00382.x
  18. Lindberg, D.R. (1992) Evolution, distribution and systematics of Haliotidae. In: Abalone of the Word: Biology Fisheries and Culture. (ed. by Shepherd, M.J., Tegner, S.A., Guzman del Proo, S.A.). pp. 3-18. Blackwell Scientific. London.
  19. Margaret, W., Marie, L.H., David, R.S. and Neil, J.G. (2011) Low to moderate levels of genetic differentiation detected across the distribution of the New Zealand abalone, Haliotis iris. Marine Biology, 158: 1417-1429. https://doi.org/10.1007/s00227-011-1659-x
  20. Maynard, B.T., Kerr, L.J., McKiernan, J.M., Jansen, E.S. and Hanna, P.J. (2005) Mitochondrial DNA sequence and gene organization in Australian backup abalone Haliotis rubra (leach). Marine Biotechnology, 7: 645-658. https://doi.org/10.1007/s10126-005-0013-z
  21. Moritz, C., Dowlin, T.E. and Brown, W.M. (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annual Review of Ecology and Systematics, 18: 269-92. https://doi.org/10.1146/annurev.es.18.110187.001413
  22. Saitou, N. and Nei, M. (1987) The Neighbor-joining Method: A new method for reconstructing phylogenetic trees1. Molecular Biology and Evolution, 4(4): 406-425.
  23. Sekino, M., Sato, S., Hong, J.S. and Li, Q. (2012) Contrasting pattern of mitochondrial population diversity between an estuarine bivalve, the Kumamoto oyster Crassostrea sikamea, an the closely related Pacific oyster C. gigas. Marine biology, 159: 2757-2776. https://doi.org/10.1007/s00227-012-2037-z
  24. Sweijd, N.A., Bowie, R.C.K., Lopata, A.L., Marinaki, A.M., Harley, E.H. and Cook, P.A. (1998) A PCR technique for forensic, species-level identification of abalone tissue. Journal of Shellfish Research, 17: 889-895.
  25. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28: 2731-2739. https://doi.org/10.1093/molbev/msr121
  26. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  27. Van Wormhoudt, A., Le Bras, Y. and Huchette, S. (2009) Haliotis marmorata from Senegal; a sister species of Haliotis tuberculata: morphological and molecular evidence. Biochemical Systematics and Ecology, 37: 747-755. https://doi.org/10.1016/j.bse.2009.12.020
  28. Van Wormhoudt, A., Roussel, V., Courtois, G. and Huchette, S. (2011) Mitochondrial DNA Introgression in the European Abalone Haliotis tuberculata tuberculata: Evidence for Experimental mtDNA Paternal Inheritance and a Natural Hybrid Sequence. Marine Biotechnology, 13: 563-574. https://doi.org/10.1007/s10126-010-9327-6
  29. White, P.S. and Densmore, L.D.III. (1992) Mitochondrial DNA isolation. In: Molecular Genetic Analysis of Populations (ed. by Hoelzel, A.R.). pp. 29-58. University Publishers, Oxford.
  30. Xin, Y., Ren, J. and Liu, X. (2011) Mitogenome of the small abalone Haliotis diversicolor Reeve and phylogenetic analysis within Gastropoda. Marine Genomics, 4: 253-262. https://doi.org/10.1016/j.margen.2011.06.005

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