Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance-based DNA barcoding

Molecular Ecology Resources

Volumn 11, Issue 5, 2011, Pages 820-830

  Liu, Jun ^a   Li, Qi ^a   Kong, Lingfeng ^a   Yu, Hong ^a   Zheng, Xiaodong ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

16S rDNA; Cytochrome c oxidase subunit I; DNA barcoding; Ostreidae; Oysters

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA; PRIMER DNA; RNA 16S;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA BARCODING; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OYSTER; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; DNA BARCODING, TAXONOMIC; DNA PRIMERS; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OSTREA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BIVALVIA; OSTREIDAE;

EID: 80051683936     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03025.x     Document Type: Article

References (60)

1. Banks MA, McGoldrick DJ, Borgeson W, Hedgecock D (1994) Gametic incompatibility and genetic divergence of Pacific and Kumamoto oysters, Crassostrea gigas and C. sikamea. Marine Biology, 121, 127-135.
2. Bernard FR, Cai YY, Morton B (1993) Catalogue of Living Marine Bivalve Molluscs of China. Hong Kong University Press, Hong Kong.
3. Bieler B, Mikkelsen PM, Lee T, O';Foighil D (2004) Discovery of the Indo-Pacific oyster Hyotissa hyotis (Linnaeus, 1758) in the Florida Keys (Biavalvia: Gryphaeidae). Molluscan Research, 24, 149-159.
4. Cross I, Rebordinos L (2006) Species identification of Crassostrea and Ostrea Oysters by polymerase chain reaction amplification of the 5S rDNA gene. Journal of AOAC International, 89, 144-148.
5. Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity, 97, 254-255.
6. Duncan KM, Martin AP, Bowen BW, DeCouet HG (2006) Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini). Molecular Ecology, 15, 2239-2251.
7. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
8. Giribet G, Okusu A, Lindgren AR et al. (2006) Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons. Proceeding of the National Academy of Sciences of the United States of America, 103, 7723-7728.
9. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
10. Gunter G (1950) The generic status of living oysters and the scientific name of the common American species. The American Midland Naturalist, 43, 438-449.
11. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
12. Harry HW (1985) Synopsis of the supraspecific classification of living oysters (Bivalvia: Gryphaeidae and Ostreidae). Veliger, 28, 121-158.
13. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, 313-321.
14. Hebert PDN, Stockle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. Plos Biology, 2, e312.
15. Jozefowicz CJ, Ó Foighil D (1998) Phylogenetic analysis of southern hemisphere flat oysters based on partial mitochondrial 16S rDNA gene sequences. Molecular Phylogenetics and Evolution, 10, 426-435.
16. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
17. Klinbunga S, Ampayup P, Tassanakajon A, Jarayabhand P, 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.
18. Klinbunga S, Khamnamtong N, Tassanakajon A, Puanglarp N, Jarayabhand P (2003) Molecular genetic identification tools for three commercially cultured oysters (Crassostrea belcheri, Crassostrea iredalei, and Saccostrea cucullata) in Thailand. Marine Biotechnology, 5, 27-36.
19. Klinbunga S, Khamnamtong B, Puanglarp N et al. (2005) Molecular taxonomy of cupped oysters (Crassostrea, Saccostrea, and Striostrea) in Thailand based on COI, 16S, and 18S rDNA polymorphism. Marine Biotechnology, 7, 306-317.
20. Lam K (2009) Oysters (Bivalvia: Ostreidae and Gryphaeidae) recorded from Malaysia and Singapore. The Raffles Bulletin of Zoology, 57, 481-494.
21. Lam K, 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.
22. Lam K, Morton B (2006) Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rock oysters (Ostreidae: Saccostrea species). Journal of Molluscan Studies, 72, 235-245.
23. Lapègue S, Batista RM, Heurtebise S, Yu ZN, Boudry P (2004) Evidence for the presence of the Portuguese oyster, Crassostrea angulata, in Northern China. Journal of Shellfish Research, 23, 759-763.
24. Li X, Qi Z (1994) Studies on the comparative anatomy, systematic classification and evolution of Chinese oysters. Studia Marina Sinica, 35, 143-173.
25. Li Q, Yu H, Yu RH (2006) Genetic variability assessed by microsatellites in cultured populations of the Pacific oyster (Crassostrea gigas) in China. Aquaculture, 259, 95-102.
26. Littlewood DTJ (1994) Molecular phylogenetics of cupped oysters based on partial 28S rRNA gene sequences. Molecular Phylogenetics and Evolution, 3, 221-229.
27. López-Flores I, de la Herrán R, Garrido-Ramos MA et al. (2004) The molecular phylogeny of oysters based on a satellite DNA related to transposons. Gene, 339, 181-188.
28. López-Flores I, Ruiz-Rejón C, Cross I et al. (2010) Molecular characterization and evolution of an interspersed repetitive DNA family of oysters. Genetica, 138, 1211-1219.
29. Matsumoto M (2003) Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences. Molecular Phylogenetics and Evolution, 27, 429-440.
30. Meier R, Zhang GY, Ali F (2008) The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Systematic Biology, 57, 809-813.
31. Melo CMR, Silva FC, Gomes CHAM, Solé-Caca AM, Lazoski C (2010) Crassostrea gigas in natural oyster banks in southern Brazil. Biological Invasions, 12, 441-449.
32. deMelo AGC, Varela ES, Beasley CR et al. (2010) Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea). Genetics Molecular Biology, 33, 564-572.
33. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Plos Biology, 3, e422.
34. Milbury CA, Gaffney PM (2005) Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Marine Biotechnology, 7, 697-712.
35. Morton B (2004) The oysters of Hong Kong (Bivalvia: Ostreidae and Gryphaeidae). The Raffles Bulletin of Zoology, 52, 11-28.
36. Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Molecular Systematics (eds Hillis DM, Moritz C & Mable BK), pp. 205-247. Sinauer & Associates Inc., Sunderland, MA.
37. Plazzi F, Passamonti M (2010) Towards a molecular phylogeny of Mollusks: bivalves' early evolution as revealed by mitochondrial genes. Molecular Phylogenetics and Evolution, 57, 641-657.
38. Polson MP, Hewson WE, Eernisse DJ, Baker PK, Zacherl D (2009) You say Conchaphila, I say lurida: molecular evidence for restricting the Olympia oyster to temperate western north America. Journal of Shellfish Research, 28, 11-21.
39. Posada D (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
40. Qi Z (1989) Mollusk of Yellow Sea and Bohai Sea. Agricultural Publishing House, Beijing (In Chinese).
41. Reece KS, Cordes JF, Stubbs JB, Hudson KL, Francis EA (2008) Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species. Marine Biology, 153, 709-721.
42. Ren JF (2008) Researches on molluscan mitogenomics and molecular phylogenetics. PhD Dissertation. Graduate School of Chinese Academy of Sciences, Beijing.
43. Ren JF, Liu X, Zhang GF, Liu B, Guo XM (2009) "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes. BMC genomics, 10, 84.
44. Ren JF, Liu X, Zhang GF, Liu B, Guo XM (2010) Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evolutionary Biology, 10, 394.
45. Ruesink JL, Lenihan HS, Trimble AC et al. (2005) Introduction of non-native oysters: ecosystem effects and restoration implications. Annual Review of Ecology, Evolution, and Systematics, 36, 643-689.
46. Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature, 435, 17.
47. Seifert KA, Samson RA, deWaard JR et al. (2007) Prospects for fungus identification using co1 DNA barcodes, with Penicillium as a test case. Proceeding of the National Academy of Sciences of the United States of America, 104, 3901-3906.
48. Tamura K, Dudley J, Nei M, Kumar S (2007) mega4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
49. Tang RWK, Yau C, Ng WC (2010) Identification of stomatopod larvae (Crusacea: Stomatopoda) from Hong Kong waters using DNA barcodes. Molecular Ecology Resources, 10, 439-448.
50. Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choices. Nucleic Acids Research, 22, 4673-4680.
51. Wang HY, Guo XM (2008b) Identification of Crassostrea ariakensis and related oysters by multiplex species-specific PCR. Journal of Shellfish Research, 27, 481-487.
52. Wang HY, Guo XM, Zhang GF, Zhang FS (2004) Classification of jingjiang oysters Crassostrea rivularis (Gould, 1861) from China, based on morphology and phylogenetic analysis. Aquaculture, 242, 137-155.
53. Wang HY, Zhang GF, Liu X, Guo XM (2008a) Classification of common oysters from north China. Journal of Shellfish Research, 27, 495-503.
54. Ward BD, Holmes BH (2007) An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes, 7, 899-907.
55. Wu XY, Xu XD, Yu ZN, Wei ZP, Xia JJ (2010) Comparison of seven Crassostrea mitogenomes and phylogenetic analyses. Molecular Phylogenetics and Evolution, 57, 448-454.
56. Xu F, Huang X (1993) The new record of Ostreacea in China sea. Studia Marina Sinica, 4, 175-179.
57. Yu H, Li Q (2011) Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS ONE, 6, e16147.
58. Yu Z, Kong X, Zhang L, Guo X, Xiang J (2003) Taxonomic status of four Crassostrea oysters from China as inferred from mitochondrial DNA sequences. Journal of Shellfish Research, 22, 31-38.
59. Yu ZN, Wei ZP, Kong XY, Shi W (2008) Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss for" genome rearrangement in Crassostrea. BMC Genomics, 9, 477.
60. Zhang X, Lou Z (1956) Studies on oysters in China. Acta Zoologica Sinica, 8, 65-94.