YU Da-hui, LI You-ning, Wu Kai-chang. Analysis on sequence variation of ITS 2 rDNA in Pinctada fucata from China, Japan and Australia[J]. South China Fisheries Science, 2005, 1(2): 1-6.
Citation: YU Da-hui, LI You-ning, Wu Kai-chang. Analysis on sequence variation of ITS 2 rDNA in Pinctada fucata from China, Japan and Australia[J]. South China Fisheries Science, 2005, 1(2): 1-6.

Analysis on sequence variation of ITS 2 rDNA in Pinctada fucata from China, Japan and Australia

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  • Received Date: April 10, 2005
  • The internal transcribed spacer 2 (ITS 2) and the flanked genes fragment in pearl oyster Pinctada fucata was studied, including samples collected from three geographic localities: China, Japan and Australia.The PCR product contains 5.8 S gene, partial sequence, ITS 2, complete sequence and 28 S gene, partial sequence. Total 16 genotypic sequences were analyzed. Sequences of 5.8 S and 28 S segments are highly conservative and are 64 and 249 bp long, respectively with exclusion of primers base pairs. The length of ITS 2 varies from 230 to 237 bp with twenty mutation sites, including twelve insertion/deletion sites, four singletons and four parsimony informative sites, showing highly genetic variation. The GC contents of 5.8 S (59.4%) and 28 S (58.1%) segments are higher than AT contents, and also higher than that of ITS 2 (51.3%~52.0%). Base frequency of T is the lowest in 28 S segment and the base frequency of A the lowest in 5.8 S. The genetic distances within and among the three populations are low (0.010~0.013) and overlapped. The genotypic data reveals that one genotype is shared by three populations and one shared by Japanese and Australian populations; most genotypes are population specific. The sequence information indicates that there are no common mutation sites for individual population. These findings suggest that the three populations may diverge at recent and/or there are gene flows among them.Thus selective breeding may profit from the high level of genetic variation in the populations of P. fucata.

  • [1]
    Shirai S. Pearls and pearl oysters of the world [M]. Okinawa: Marine Planning Co., 1994. 108.
    [2]
    Wada K T. Genetic variability at four polymorphic loci in Japanese pearl oysters, Pinctada fucata martensii, selected for six generations[J]. Aquac, 1986, 59(2): 139-146. doi: 10.1016/0044-8486(86)90126-2
    [3]
    Velayudhan T S, Chellam S, Dharmaraj S, et al. Comparison of growth and shell attributes of four generations of the pearl oyster Pinctada fucata (Gould) produced in the hatchery[J]. Indian J Fish, 1996, 43(1): 69-77. https://www.semanticscholar.org/paper/Comparison-of-growth-and-shell-attributes-of-four-Velayudhan-Chellam/368e4f4dd7ff6f5a6f52d0c2743fb9bd27b3df26
    [4]
    O'Connor W A, Lawler N F. Reproductive condition of the pearl oyster, Pinctada imbricata, Röding, in Port Stephens, New South Wales, Australia[J]. Aquac Res, 2004, 35(4): 385-396. doi: 10.1111/j.1365-2109.2004.01027.x
    [5]
    Urban H J. Culture potential of the pearl oyster (Pinctada imbricata) from the Caribbean. I. Gametogenic activity, growth, mortality and production of a natural population[J]. Aquac, 2000, 189(3-4): 361-373. doi: 10.1016/S0044-8486(00)00393-8
    [6]
    Hillis D M, Dixon M T. Ribosomal DNA: Molecular evolution and phylogenetic inference[J]. Quaterly Review of Biol, 1991, 66(4): 411-453. doi: 10.1086/417338
    [7]
    Thompson J D, Gibson T J, Plewniak F, et al. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res, 1997, 25(24): 4876-4882. doi: 10.1093/nar/25.24.4876
    [8]
    Kumar S, Tamura K, Nei M. MEGA3: Molecular evolutionary genetics analysis software[M]. Tempe, Arizona: Arizona State University, USA, 2003.
    [9]
    Chu K H, Li C P, Ho H Y. The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic analyses in Crustacea[J]. Mar Biotech, 2001, 3(4): 355-361. doi: 10.1007/s10126001-0014-5
    [10]
    Beauchamp K A, Powers D A A. Sequence variation of the first internal transcribed spacer (ITS-1) of ribosomal DNA in ahermatypic corals from California[J]. Mol Mar Biol Biotech, 1996, 5(3): 357-362. https://pubmed.ncbi.nlm.nih.gov/8983201/
    [11]
    Chen C A, Chen C P, Fan T Y, et al. Nucleotide sequences of ribosomal internal transcribed spacers and their utility in distinguishing closely related Perinereis polychaetes (Annelida; Polychaeta; Nereididae)[J]. Mar Biotech, 2002, 4(1): 17-29. doi: 10.1007/s10126-001-0069-3
    [12]
    Hedgecock D, Li G, Banks M A, et al. Occurrence of the Kumamoto oyster Crassostrea sikamea in the Ariake Sea Japan. Mar Biol, 1998, 133(1): 65-68. doi: 10.1007/s002270050443
    [13]
    Karvonen P, Szmidt A E, Savolainen O. Length variation in the internal transcribed spacers of ribosomal DNA in Picea abies and related species[J]. Theoretical and Applied Genetics, 1994, 89(9): 969-974. doi: 10.1007/BF00224526
    [14]
    López-Piňón M J, Insua A, Méndez J. Identification of four scallop species using PCR and restriction analysis of the ribosomal DNA internal transcribed spacer region[J]. Mar Biotech, 2002, 4(5): 495-502. doi: 10.1007/s10126-002-0030-0
    [15]
    Remigio E A, Blair D. Relationships among problematic North American stagnicoline snails (Pulmonata: Lymnaeidae) reinvestigated using nuclear ribosomal DNA internal transcribed spacer weuences[J]. Can J Zool, 1997, 75(11): 1540-1545. doi: 10.1139/z97-779
    [16]
    Colgan D J, Ponder W F. Genetic discrimination of morphologically similar, sympatric species of pearl oysters (Mollusca: Bivalvia: Pinctada) in eastern Australia[J]. Mar Freshw Res, 2002, 53(2): 697-709. doi: 10.1071/MF99178
    [17]
    Atsumi T, Komaru A, Okamoto C. Genetic relationship among the Japanese pearl oyster Pinctada fucata martensii and other pearl oysters[J]. 水產育種, 2004, 33(2): 135-142.
    [18]
    Harris D J, Crandall K A. Introgenomic variation within ITS 1 and ITS 2 of freshwater crayfishes (Decapoda: Cambaridae): Implications for phylogenetic and microsatellite studies[J]. Mol Biol Evolution, 2000, 17(2): 284-291. doi: 10.1093/oxfordjournals.molbev.a026308
    [19]
    何毛贤, 黄良民. 长耳珠母贝核rRNA基因ITS-2序列分析[J]. 热带海洋学报, 2004, 23(5): 81-84. doi: 10.3969/j.issn.1009-5470.2004.05.011
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