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Genetic identification of two species of Pleuronichthys by DNA barcoding

  • Hui Zhang (张辉)
  • Yan Zhang (张岩)
  • Tianxiang Gao (高天翔)
  • Pengfei Li (李鹏飞)
  • Hanxiang Xu (徐汉祥)
Biology

Abstract

DNA barcoding is a new method for biological taxonomy, offering the ability to identify species from fragments in any life-history stage. Pleuronichthys cornutus and P. japonicus are two morphologically similar species. Pleuronichthys japonicus has never been found previously in China. However, in this study, we identified both species using DNA barcoding (cytochrome c oxidase subunit I (COI)), the mtDNA control region and cytochrome b. The results reveal that: 1) intraspecific variation in the DNA barcode is much less than interspecific variation; 2) the two morphologically similar species were placed into separate clades distinguishable by high bootstrap values; 3) COI barcodes are more powerful for identifying the two species than the other two mtDNA fragments.

Keyword

Pleuronichthys DNA barcoding COI CR Cyt b 

References

  1. Barrett R D H, Hebert P D N. 2005. Identifying spiders through DNA barcodes. Can. J. Zool., 83: 481–491.CrossRefGoogle Scholar
  2. Cooper J K, Sykes G, King S, Cottrill K, Ivanova N V, Hanner R, Ikonomi P. 2007. Species identification in cell culture: a two-pronged molecular approach. In Vitro Cell. Dev. Biol.-An., 43: 344–351.CrossRefGoogle Scholar
  3. Felsenstein J, Churchill G A. 1996. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol. Biol. Evol., 13: 93–104.Google Scholar
  4. Gao T X, Chen S Q, Liu J Q, Zhang Y P. 2004. Comparative analysis of mitochondrial DNA sequences between Verasper variegates and V. moseri. High Tech. Letters, 14: 329–334. (in Chinese)Google Scholar
  5. Hajibabaei M, de Waard J R, Ivanova N V, Ratnasingham S, Dooh R T, Kirk S L, Mackie P M, Hebert P D N. 2005. Critical factors for assembling a high volume of DNA barcodes. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 360: 195 9–196 7.Google Scholar
  6. Hajibabaei M, Smith M A, Janzen D H, Rodriguez J J, Whitfield J B, Hebert P D N. 2006. A minimalist barcode can identify a specimen whose DNA is degraded. Mol. Ecol. Notes, 6: 959–964.CrossRefGoogle Scholar
  7. Han Z Q, Gao T X, Yanagimato T, Sakurai Y. 2008. Genetic population structure of Nibea albiflora in Yellow Sea and East China Sea. Fish. Sci., 74: 544–552.CrossRefGoogle Scholar
  8. Hebert P D N, Penton E H, Burns J M, Janzen D H, Hallwachs W. 2004a. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci., 101: 14 812–14 817.CrossRefGoogle Scholar
  9. Hebert P D N, Stoeckle M Y, Zemlak T S, Francis C M. 2004b. Identification of birds through DNA barcodes. Plos. Biology, 2: 1 657–1 663.CrossRefGoogle Scholar
  10. Hebert P D N, Cywinska A, Ball S L, deWaard J R. 2003a. Biological identifications through DNA barcodes. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 270: 313–321.CrossRefGoogle Scholar
  11. Hebert P D N, Ratnasingham S, deWaard J R. 2003b. Barcoding animal life: cytochrome c oxidase subunit I divergences among closely related species. Philos. Trans. R. Soc. Lond. B. Biol. Sci. (Supp.1), 270: S96–S99.CrossRefGoogle Scholar
  12. Huelsenbeck J P, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17: 754–755.CrossRefGoogle Scholar
  13. Li S Z. 1995. Fauna Sinica: Ostichthyes: Pleuronectiformes. Science Press, Beijing, China. p.238–241. (in Chinese)Google Scholar
  14. Meyer A. 1993. Evolution of Mitochondrial DNA in Fishes. Elsevier Press, Amsterdam, Holland. p.1–36.Google Scholar
  15. Meyer C P, Paulay G. 2005. DNA Barcoding: error rates based on comprehensive sampling. Plos. Biol., 3: e422.CrossRefGoogle Scholar
  16. Nakabo T. 2000. Fishes of Japan with Pictorial Keys to the Species (2nd Edition). Tokai University Press, Kanagawaken, Japan. p.1 372.Google Scholar
  17. Posada D, Crandall K A. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics, 14: 817–818.CrossRefGoogle Scholar
  18. Pyle R L, Earle J L, Greene B D. 2008. Five new species of the damselfish genus Chromis (Perciformes:Labroidei: Pomacentridae) from deep coral reefs in the tropical western Pacific. Zootaxa, 1 671: 3–31.Google Scholar
  19. Ratnasingham S, Hebert P D N. 2007. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes, 7: 355–364.CrossRefGoogle Scholar
  20. Ronquist F, Huelsenbeck J P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed model. Bioinformatics, 19: 1 572–1 574.CrossRefGoogle Scholar
  21. Rozas J, Rozas R. 1995. DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data. Comput. Applic. Biosci., 11: 621–625.Google Scholar
  22. Sambrook J. 1989. Molecular Cloning: A Laboratory Manual, 2nd Edition. Cold Spring Harbor Laboratory Press, New York, America.Google Scholar
  23. Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C. 1997. Mammalian mitochondrial D-loop region structure analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene, 205: 125–140.CrossRefGoogle Scholar
  24. Schneider S, Roessli D, Excoffier L. 2000. ARLEQUIN, Version 2.0: A Software for Population Genetic Data Analysis. University of Geneva, Geneva, Switzerland.Google Scholar
  25. Suzuki S, Kawashima T, Nakabo T. 2009. Taxonomic review of East Asian Pleuronichthys (Pleuronectiformes: Pleuronectidae), with description of a new species. Ichyhyol. Res., 56: 276–291.CrossRefGoogle Scholar
  26. Swofford D L. 2002. PAUP: Phylogenetic Analysis Using Parsimony Version 4. Sinauer, Sunderland, Massachusetts.Google Scholar
  27. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol., 24: 1 596–1 599.CrossRefGoogle Scholar
  28. Tautz D, Arctander P, Minelli A, Thomas R H, Vogler A P. 2002. DNA points the way ahead in taxonomy. Nature, 418: 479.CrossRefGoogle Scholar
  29. Wang Y J, Tabeta O, Ren Y P. 1999. Age and growth of the finspotted flounder Pleuronichthys sp. in the East China Sea. J. Ocean Univ. Qingdao, 29: 604–610. (in Chinese)Google Scholar
  30. Ward R D, Zemlak T S, Innes B H, Last P R, Hebert P D N. 2005. DNA barcoding Australia’s fish species. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 360: 1 847–1 857.Google Scholar
  31. Ward R D, Holmes B H, White W T, Last P R. 2008. DNA barcoding of shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquatic. biology, 3: 71–78.CrossRefGoogle Scholar
  32. Zhang Y, Xiao Y S, Gao T X, Yu H. 2009. Comparative analysis of mtDNA gene sequences between two species of Pleuronectes. J. Fish. China, 33: 210–207. (in Chinese)Google Scholar

Copyright information

© Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Hui Zhang (张辉)
    • 1
  • Yan Zhang (张岩)
    • 2
  • Tianxiang Gao (高天翔)
    • 1
  • Pengfei Li (李鹏飞)
    • 3
  • Hanxiang Xu (徐汉祥)
    • 3
  1. 1.Fisheries CollegeOcean University of ChinaQingdaoChina
  2. 2.Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
  3. 3.Marine Fisheries Research Institute of Zhejiang ProvinceZhoushanChina

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