Genetic Relationships of Four Korean Oysters Based on RAPD and Nuclear rDNA ITS Sequence Analyses

  • Kim, Woo-Jin (Biotechnology Research Institute, National Fisheries Research and Development Institute) ;
  • Lee, Jeong-Ho (Genetics and Breeding Research Center, National Fisheries Research and Development Institute) ;
  • Kim, Kyung-Kil (Biotechnology Research Institute, National Fisheries Research and Development Institute) ;
  • Kim, Young-Ok (Biotechnology Research Institute, National Fisheries Research and Development Institute) ;
  • Nam, Bo-Hye (Biotechnology Research Institute, National Fisheries Research and Development Institute) ;
  • Kong, Hee-Jeong (Biotechnology Research Institute, National Fisheries Research and Development Institute) ;
  • Jung, Hyung-Taek (Biotechnology Research Institute, National Fisheries Research and Development Institute)
  • 발행 : 2009.05.31

초록

Random amplified polymorphic DNA (RAPD) marker and sequence analyses of the internal transcribed spacer (ITS) region of ribosomal DNA were used to assess phylogenetic relationships of four Korean oyster species. The average number of species-specific markers identified from five universal rice primers (URPs) by RAPD-PCR was 1.8 for Crassostrea gigas, 3.2 for C. nippona, 3.6 for C. ariakensis, and 4.6 for Ostrea denselamellosa. The length of the ITS (ITS1-5.8S-ITS2) region ranged from 1,001 to 1,206 bp (ITS1, 426-518 bp; 5.8S, 157 bp; and ITS2, 418-536 bp), while the GC content ranged from 55.5-61.1% (ITS1, 56.8-61.8%; 5.8S, 56-57.3%; and ITS2, 54.1-62.2%). A phylogenetic analysis of the oysters based on our RAPD, ITS1, and ITS2 sequence data revealed a close relationship between C. gigas and C. nippona and a distant relationship between the genera Crassostrea and Ostrea. Our results indicated that RAPD and ITS sequence analysis was a useful tool for the elucidation of phylogenetic relationships and for the selection of species-specific markers in Korean oysters.

키워드

참고문헌

  1. An, H.S., Park, D.W. and Jee, Y.J. (1999) Genetic variation in populations of the oyster (Crassostrea nippona) as examined by mitochondria DNA sequence analysis. Bulletin of National Fisheries Research and Development Institute, 57: 73-78.
  2. Asahida, T., Kobayashi, T., Saitoh, K. and Nakayama, I. (1996) Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentration of urea. Fisheries Science, 62: 727-730.
  3. Boudry, P., Heurtebise, S. and Lapegue, S. (2003) Mitochondrial and nuclear DNA sequence variation of presumed Crassostrea gigas and Crassostrea angulata specimens: a new oyster species in Hong Kong. Aquaculture, 228: 15-25. https://doi.org/10.1016/S0044-8486(03)00443-5
  4. Caetano-Anolles, G., Bassam, B.J. and Gresshoff, P.M. (1992) Primer-template interactions during DNA amplification fingerprinting with single arbitrary oligonucleotides. Molecular and General Genetics, 235: 157-165. https://doi.org/10.1007/BF00279356
  5. Chen, C.A, Willis, B.L. and Miller, D.J. (1996) Systematic relationships of the tropical corallimorpharians (Cnidaria: Anthozoa): utility of the 5.8S and internal transcribed spacers (ITS) of ribosomal DNA units. Bulletin of Marine Science, 59: 196-208.
  6. Cheng, H.L., Meng, X.P., Ji, H.J., Dong, Z.G. and Chen, S.Y. (2006) Sequence analysis of the ribosomal DNA internal transcribed spacers and 5.8S ribosomal RNA gene in representatives of the clam family Veneridae (Mollusca: Bivalvia). Journal of Shellfish Research, 25: 833-839.
  7. Chu, K.H., Li, C.P. and Ho, H.Y. (2001) The first internal transcribed spacer (ITS1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in Crustacea. Marine Biotechnology, 3: 355-361. https://doi.org/10.1007/s10126001-0014-5
  8. Crossland, S., Coates, D., Grahame, J. and Mill, P.J. (1993) Use of random amplified polymorphic DNAs (RAPDs) in separating two sibling species of Littorina. Marine Ecology Progress Series, 96: 301-305. https://doi.org/10.3354/meps096301
  9. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39: 783-791. https://doi.org/10.2307/2408678
  10. Fernandez, A., Garcia, T., Asensio, L., Rodriguez, M.A., Gonzalez, I., Hernandez, P.E. and Martin, R. (2001) PCR-RFLP analysis of the internal transcribed spacer (ITS) region for identification of 3 clam species. Journal of Food Science, 66: 657-661. https://doi.org/10.1111/j.1365-2621.2001.tb04617.x
  11. Freire, R. (2002) Analisis de secuencias de and ribosomico enberberechos y mejillones de la costa europea. PhD. Thesis, University da Coruna, Spain.
  12. Gaffney, P.M., Jung, H.T., Kim, W.J., Varney, R. and Milbury, C. (2006) Development and application of type I markers for linkage mapping and population genetics in Crassostrea species. Journal of Shellfish Research, 25: 727.
  13. He, M.X., Huang, L.M., Shi, J.H. and Jiang, Y.P. (2005) Variability of ribosomal DNA ITS-2 and its utility in detecting genetic relatedness of Pearl Oyster. Marine Biotechnology, 7: 40-45. https://doi.org/10.1007/s10126-004-0003-6
  14. Heipel, D.A, Bishop, J.D.D., Brand, A.R. and Thorpe, J.P. (1998) Population genetic differentiation of the great scallop Pecten maximus in western Britian investigated by randomly amplified polymorphic DNA. Marine Ecology Progress Series, 162: 163-171. https://doi.org/10.3354/meps162163
  15. Hillis, M.D.M. and Davis, S.K. (1998) Ribosomal DNA: intraspecific polymorphism, concerted evolution, and phylogeny reconstruction. Systematic Zoology, 37: 63-66. https://doi.org/10.2307/2413191
  16. Hsueh, J.Y., Jr Bohm, R.P., Didier, P.J., Tang, X., Lasbury, M.E., Li, B., Jin, S., Bartlett, M.S., Smith, J.W. and Lee, C.H. (2001) Internal transcribed spacer regions of rRNA genes of Pneumocystis carinii from monkeys. Clinical and Diagnostic Laboratory Immunology, 8: 503-508.
  17. Insua, A., Lopez-Pinon, M.J., Freire, R. and Mendez, J. (2003) Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae). Genome, 46: 595-604. https://doi.org/10.1139/g03-045
  18. Jung, H.T., Kim, W.J. and Gaffney, P.M. (2006) Development of single nucleotide polymorphisms (SNPs) in Crassostrea ariakensis and related Crassostrea species. Journal of Shellfish Research, 25: 742.
  19. Kang, H.W., Park, D.S., Go, S.J. and Eun, M.Y. (2002) Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequence of Korean weedy rice. Molecular and Cells, 13: 281-287.
  20. Kenchington, E., Bird, C.J., Osborne, J. and Reith, M. (2002) Novel repeat elements in the nuclear ribosomal RNA operon of the flat oysters Ostrea edulis C. Linnaeus, 1785 and O. angasi Sowerby, 1871. Journal of Shellfish Research, 212: 697-705.
  21. Kim, S.H., Park, M.S., Kim, Y.H. and Park, D.W. (1997) Genetic analysis of mitochondrial DNA from Korea oysters, Crassostrea gigas. Journal of Korean Fisheries Society, 30: 804-808.
  22. Kim, W.J., Kim, K.K., Lee, J.H. and Park, D.W. (2003) Identification of potential species-specific marker in several fish species by RAPD using universal rice primers. Journal of Korean Fisheries Society, 36: 317-320. https://doi.org/10.5657/kfas.2003.36.3.317
  23. King, T.L., Eackles, M.S., Gjetvaj, B. and Hoeh, V. (1999) Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): conservation implications of range discontinuity. Molecular Ecology, 8: S65-S78. https://doi.org/10.1046/j.1365-294X.1999.00784.x
  24. Klinbunga, S., Ampayup, P., Tassanakajon, A., Jarayabhand, P. and Yoosukh, W. (2001) Genetic diversity and molecular markers of cupped oysters (Genera Crassostrea, Saccostrea, and Striostrea) in Thailand revealed by randomly amplified polymorphic DNA analysis. Marine Biotechnology, 3: 133-144. https://doi.org/10.1007/s101260000057
  25. Klinbunga. S., Boonyapakdee, A. and Pratoomchat, B. (2000) Genetic diversity and species-diagnostic markers of mud crabs (Genus Scylla) in eastern Thailand determined by RAPD analysis. Marine Biotechnology, 2: 180-187.
  26. Kumar, S., Tamura, K. and Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5: 150-163. https://doi.org/10.1093/bib/5.2.150
  27. Kuwahara, T., Norimatsu, I., Nakayama, H., Akimoto, S., Kataoka, K., Arimochi, H. and Ohnishi, Y. (2001) Genetic variation in 16S-23S rDNA internal transcribed spacer regions and the possible use of this genetic variation for molecular diagnosis of Bacteroides species. Microbiology and Immunology, 45: 191-199.
  28. Lam, K. and Morton, B. (2003) Mitochondrial DNA and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aquaculture, 228: 1-13. https://doi.org/10.1016/S0044-8486(03)00215-1
  29. Lee, S.Y., Park, W.P., An, H.S. and Kim, S.H. (2000) Phylogenetic relationship among four species of Korean oysters based on mitochondria 16S rDNA and COI gene. Korean Journal of Systematic Zoology, 16: 203-211.
  30. Liu, Z.J. and Cordes, J.F. (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238: 1-37. https://doi.org/10.1016/j.aquaculture.2004.05.027
  31. Ministry of Maritime Affairs and Fisheries (2006) Fisheries Statistics of Korea 2006. Seoul, Korea. (http://www.momaf.go.kr/eng/main/main.asp).
  32. Morgan, J.A. and Blair, D. (1998) Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. Journal of Molecular Evolution, 47: 406-419. https://doi.org/10.1007/PL00006398
  33. Morgan, T.S. and Rogers, A.D. (2001) Specificity and sensitivity of microsatellite markers for the identification of larvae. Marine Biology, 139: 967-973. https://doi.org/10.1007/s002270100589
  34. Nazar, R.N. (1984) The ribosomal 5.8S RNA: eukaryotic adaptation or processing variant. Canadian Journal of Biochemistry and Cell Biology, 62: 311-320. https://doi.org/10.1139/o84-044
  35. Nei, M. (1987) Molecular Evolutionary Genetics. pp. 106-107. Columbia Press, New York.
  36. Odorico, D. and Miller, D.J. (1997) Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): variation consistent with reticulate evolution. Molecular Biology and Evolution, 14: 465-473. https://doi.org/10.1093/oxfordjournals.molbev.a025783
  37. Park, H.S. and Kim, S.H. (1995) Mitochoncrial DNA variation in oyster (Crassostrea gigas Thunberg and C. nippona Seki) populations from Korea and Japan. Korean Journal of Systematic Zoology, 11: 235-242.
  38. Patwary, M.U., Kenchington, E.L., Bird, C.J. and Zouros, E. (1994) The use of random amplified polymorphic DNA markers in genetic studies of the sea scallop Placopecten magellanicus (Gmelin, 1971). Journal of Shellfish Research, 13: 547-553.
  39. Posada, D. and Grandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinfomatics Application Notes, 14: 817-818. https://doi.org/10.1093/bioinformatics/14.9.817
  40. Sneath, P.H.A. and Sokal, R.R. (1973) Numerical Taxonomy. 573 p. Freeman, San Francisco.
  41. Takabayashi, M., Carter, D., Ward, S. and Hoegh-Guldberg, O. (1998) Inter- and intra-specific variability in ribosomal DNA sequence in the internal transcribed spacer region. In: Proceeding of the Australlian Coral Reef Society 75th Anniversary Conference. pp. 241-248. School of Marine Science The University of Queensland, Brisbane.
  42. Tassanakaion, A., Pongsomboom, S., Rimphanitchayakit, V., Jarayabhand, P. and Boonsaeng, V. (1997) Random amplified polymorphic DNA (RAPD) markers for determination of genetic variation in wild populations of the tiger prawn (Penaeus monodon) in Thailand. Molecular Marine Biology and Biotechnology, 6: 110-115.
  43. Ursi, D., Vandenberghe, A. and De Wachter, R. (1983) Nucleotide sequences of the 5.8S rRNAs of a mollusc and a porifer, and considerations regarding the secondary structure of 5.8S rRNA and its interaction with 28S rRNA. Nucleic Acids Research, 11: 8111-8120. https://doi.org/10.1093/nar/11.22.8111
  44. Wang, H., Guo, X., Zhang, G. and Zhang, F. (2004) Classification of jinjiang oysters Crassostrea rivularis (Gould, 1861) from China, based on morphology and phylogenetic analysis. Aquaculture, 242: 137-155. https://doi.org/10.1016/j.aquaculture.2004.09.014
  45. White, T.J., Bruns, T., Lee, S. and Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols, A Guide to Methods and Applications. (ed, by Innis, M.A., Gelfand, D.H., Sninsky, J.J. and White, T.J.) pp. 315-322. Academic Press, San Diego.
  46. Williams, J.G.K., Kubelic, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18: 6531-6535. https://doi.org/10.1093/nar/18.22.6531
  47. Yu, E.T., Juinio-Menez, M.A. and Monje, V.D. (2000) Sequence variation in the ribosomal DNA internal transcribed spacer of Tridacna crocea. Marine Biotechnology, 2: 511-516. https://doi.org/10.1007/s101260000033