Sequence polymorphism in a novel noncoding region of Pacific oyster mitochondrial DNA

• Autorzy: Aranishi F , Okimoto T
• Języki publikacji: EN

Abstrakty

EN

Nucleotide sequence polymorphism in a 641-bp novel major noncoding region of mitochondrial DNA (mtDNA-NC) of the Pacific oyster Crassostrea gigas was analysed for 29 cultured individuals within the Goseong population. A total of 30 variable sites were detected, and the relative frequency of nucleotide alteration was determined to be 4.68. Alterations were mostly single nucleotide substitutions. Transition, transversion, both transition and transversion, and both transversion and nucleotide deletion were observed at 18, 9,2 and 1 sites, respectively. Among 29 specimens, 22 haplotypes were identified, and pairwise genetic diversity of haplotypes was calculated to be 0.988 from multiple sequence substitutions using the two-parameter model. A phylogenetic tree, obtained for haplotypes by the neighbor-joining method, showed a single cluster of linkages. The cluster comprised 11 haplotypes associating with 14 specimens, while the other 11 haplotypes associating with 15 specimens were scattered. This mtDNA-NC presenting a high nucleotide sequence polymorphism is a potential mtDNA control region. It therefore can serve as a genetic marker for intraspecies phylogenetic analysis of the Pacific oyster and is more useful than the less polymorphic mtDNA coding genes.

Słowa kluczowe

EN

polymorphism; control region; sequence polymorhism; non-coding region; mitochondrial DNA; oyster; Pacific oyster; Crassostrea gigas; nucleotide sequence

• Wydawca: -
• Czasopismo: Journal of Applied Genetics
• Rocznik: 2005
• Tom: 46
• Numer: 2
• Opis fizyczny: p.201-206,fig.,ref.

Twórcy

autor

Aranishi F

• Department of Biological and Environment Sciences, Miyazaki University, Miyazaki 8892192, Japan

autor

Okimoto T

• Department of Biological and Environment Sciences, Miyazaki University, Miyazaki 8892192, Japan

Bibliografia

• Aranishi F, Okimoto T, 2004. Genetic relationship between cultured populations of Pacific oyster revealed by RAPD analysis. J Appl Genet 45- 435-444.
• Boudry P, Heurtebise S, Collet B, Cornette F, Gerard G, 1998. Differentiation between populations of the Portuguese oyster, Crassostrea angulata (Lamarck) and the Pacific oyster, Crassostrea gigas (Thunberg), revealed by mtDNA RFLP analysis. J Exp Mar Bio Ecol 226: 279-291.
• Boudry P, Heurtebise S, 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.
• Brands SJ, 2004. Systema Naturae 2000. Amsterdam.
• Bruford MW, Bradley DG, Luikart G, 2003. DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 4: 900-910.
• Burzyński A, Zbawicka M, Skibiński DOF, Wenne R, 2003. Evidence for recombination of mtDNA in the marine mussel Mytilus trossulus from the Baltic. Mol Biol Evol 20: 388-392.
• Cao L, Kenchington E, Zouros E, Rodakis GC, 2004. Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics 167: 835-850.
• Chew KK, 1990. Global bivalve shellfish introductions. World Aquaculture 21: 9-22.
• Choi WJ, Chun YY, Park JH, Park YC, 1997. The influence of environmental characteristics on the fatness of Pacific oyster, Crassostrea gigas, in Hansan-Koje Bay. J Korean Fish Soc 30: 794-803 (in Korean with English abstract).
• FAO 1997. Review of the State of World Aquaculture. FAO Fisheries Circular No. 886 Rev. 1. FAO, Rome. 163 pp.
• Fujio Y, 1979. Enzyme polymorphism and population structure of the Pacific oyster, Crassostrea gigas. Tohoku J Agric Res 30: 32-42.
• Hoelzel AR, 1993. Evolution by DNA turnover in the control region of vertebrate mitochondrial DNA. Curr Opin Genet Develop 3: 891-895.
• Imai T, Sakai S, 1961. Study of breeding of Japanese oyster, Crassostrea gigas. Tohoku J Agric Res 12: 125-171.
• Kang CK, Park MS, Lee PY, Choi WJ, Lee WC, 2000. Seasonal variations in condition, reproduction activity, and biochemical composition of the Pacific oyster, Crassostrea gigas (Thunberg), in suspended culture in two coastal bays of Korea. J Shellfish Res 19: 771-778.
• Kimura M, 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
• Kumar S, Tamura K, Jakobsen BI, Nei M, 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17: 1244-1245.
• Li G, Hedgecock D, 1998. Genetic heterogeneity, detected by PCR-SSCP, among samples of larval Pacific oysters (Crassostrea gigas) supports the hypothesis of large variance in reproductive success. Can J Fish Aquat Sci 55: 1025-1133.
• Lovatelli A, 1988. Status of oyster culture in selected Asian countries. FAO, Rome.
• Matthiessen GC, 2000. Oyster Culture. Fishing News Books Series, Blackwell Publishing, Ames.
• Okoshi K, Mori K, Nomura T, 1987. Characteristics of shell chamber formation between the two local races in the Japanese oyster, Crassostrea gigas. Aquaculture 67: 313-320.
• Ozaki H, Fujio Y, 1985. Genetic differentiation in geographical populations of the Pacific oyster (Crassostrea gigas) around Japan. Tohoku J Agric Res 36:49-61.
• Page RDM, 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
• Park BH, Park MS, Kim BY, Hur SB, Kim SJ, 1989. Culture of the Pacific Oyster (Crassostrea gigas) in the Republic of Korea. FAO, Rome.
• Park MS, Lim HJ, Jo Q, Yoo JS, Jeon MJ, 1999a. Assessment of reproductive health in the wild seed oysters, Crassostrea gigas, from two locations in Korea. J Shellfish Res 18: 445-450.
• Park MS, Lyu HY, Lee TS, 1999b. Investigation on the cause of bad natural seed collection of the Pacific oyster, Crassostrea gigas: relationships between the conditions of mother shell and the viability of the released eggs and larvae based on the pathological and embryological survey. J Korean Fish Soc 32: 62-67.
• Pollock DD, Eisen JA, Doggett NA, Cummings MP, 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol 17: 1776-1788.
• Rana K, Immink A, 2001. Trends in Global Aquaculture Production: 1984-1996. FAO, Rome. http://www.fao.org/DOCREP/FIELD/006/AD742E/AD742E00.HTM.
• Ross HA, Lento GM, Dalebout ML, Goode M, Ewing G, McLaren P, et al., 2003. DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises. J Hered 94: 111-114.
• Saitou N, Nei M, 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
• Sato M, Nagashima K, 2001. Molecular characterization of a mitochondrial DNA segment from the Japanese scallop (Patinopecten yessoensis): demonstration of a region showing sequence polymorphism in the population. Mar Biotechnol 3: 370-379.
• Thompson JD, Higgins DG, Gibson TJ, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673—4680.
• Zbawicka M, Skibiński DOF, Wenne R, 2003. Doubly uniparental transmission of mitochondrial DNA length variants in the mussel Mytilus trossulus. Mar Biol 142: 455—460.