Molecules and Cells

  • 제23권2호
  • /
  • Pages.220-227
  • /
  • 2007
  • /
  • 1016-8478(pISSN)
  • /
  • 0219-1032(eISSN)
한국분자세포생물학회 (Korean Society for Molecular and Cellular Biology)
권호 표지

Identification of Genes Suitable for DNA Barcoding of Morphologically Indistinguishable Korean Halichondriidae Sponges

  • Park, Mi-Hyun (Department of Biological Sciences, Inha University) ;
  • Sim, Chung-Ja (Department of Biological Science, Hannam University) ;
  • Baek, Jina (Department of Biological Sciences, Inha University) ;
  • Min, Gi-Sik (Department of Biological Sciences, Inha University)
  • 투고 : 2006.12.07
  • 심사 : 2007.02.02
  • 발행 : 2007.04.30
⟨ 이전 논문 다음 논문 ⟩

초록

The development of suitable genetic markers would be useful for defining species and delineating the species boundaries of morphologically indistinguishable sponges. In this study, genetic variation in the sequences of nuclear rDNA and the mitochondrial cytochrome c oxidase subunit 1 and 3 (CO1 and CO3) regions were compared in morphologically indistinguishable Korean Halichondriidae sponges in order to determine the most suitable species-specific molecular marker region. The maximal congeneric nucleotide divergences of Halichondriidae sponges in CO1 and CO3 are similar to those found among anthozoan cnidarians, but they are 2- to 8-fold lower than those found among genera of other triploblastic metazoans. Ribosomal internal transcribed spacer regions (ITS: ITS1 + ITS2) showed higher congeneric variation (17.28% in ITS1 and 10.29% in ITS2) than those of CO1 and CO3. Use of the guidelines for species thresholds suggested in the recent literature indicates that the mtDNA regions are not appropriate for use as species-specific DNA markers for the Halichondriidae sponges, whereas the rDNA ITS regions are suitable because ITS exhibits a low level of intraspecific variation and a relatively high level of interspecific variation. In addition, to test the reliability of the ITS regions for identifying Halichondriidae sponges by PCR, a species-specific multiplex PCR primer set was developed.

키워드

과제정보

연구 과제 주관 기관 : Regional Research Center for Coastal Environments of the Yellow Sea (CCEYS)

참고문헌

  1. Avis, J. C. (2000) Phylogeography. The history and formation of species, p. 447, Harvard University Press, Massachusetts
  2. Chombard, C., Boury-Esnault, N., and Tillier, S. (1998) Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data. Syst. Biol. 47, 351−366
  3. Cunningham, C. W. (1997) Can tree incongruence tests predict when data should be combined? Mol. Biol. Evol. 14, 733− 740
  4. Dawson, M. N. and Jacobs, D. K. (2001) Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biol. Bull. 200, 92−96
  5. Duran, S., Giribet, G., and Turon, X. (2004a) Phylogeographical history of the sponge Crambe crambe (Porifera, Poecilosclerida): range expansion and recent invasion of the Macaronesian islands from the Mediterranean Sea. Mol. Ecol. 13, 109−122
  6. Duran, S., Pascual, M., and Turon, X. (2004b) Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge Crambe crambe (Poecilosclerida). Mar. Biol. 144, 31−35
  7. Erpenbeck, D. and van Soest, R. W. M. (2002) Family Halichondriidae Gray, 1867; in Systema Porifera, A Guide to the Classification of Sponges, Hooper, J. N. A. and van Soest, R. W. M. (eds.), pp. 787−815, Kluwer Academic, New York, Boston, Dordrecht, London and Moscow
  8. Erpenbeck, D., Breeuwer, J. A. J., van der Velde, H. C., and van Soest, R. W. M. (2002) Unraveling host and symbiont phylogenies of halichondrid sponges (Demospongiae, Porifera) using mitochondrial marker. Mar. Biol. 141, 377−386
  9. Erpenbeck, D., Knowlton, A. L., Talbot, S. L., Highsmith, R. C., and van Soest, R. W. M. [2003 (2004)] A molecular comparison of Alaskan and North East Atlantic Halichondria panicea (Pallas 1766) (Porifera: Demospongiae) populations. Boll. Mus. Ist. Univ. Genova 68, 319−325
  10. Erpenbeck, D., Hooper, J. N. A., and Worheide, G. (2006) CO1 phylogenies in diploblasts and the 'Barcoding of Life'- are we sequencing a suboptimal partition? Mol. Ecol. Notes 6, 550−553
  11. Faulkner, J. (2002) Marine natural products. Nat. Prod. Rep. 19, 1−48 https://doi.org/10.1039/b007740m
  12. France, S. and Hoover, L. L. (2002) DNA sequences of the mitochondrial CO1 gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa). Hydrobiologia 471, 149−155
  13. Hebert, P. D. N., Ratnasingham, S., and De Waard, J. R. (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B. Suppl. 270, 96−99
  14. Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., and Hallwachs, W. (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. USA 101, 14812− 14817
  15. Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., and Francis, C. M. (2004b) Identification of birds through DNA barcodes. PLoS Biol. 2, e312 https://doi.org/10.1371/journal.pbio.0020312
  16. Holland, B. S., Dawson, M. N., Crow, G. L., and Hofmann, D. K. (2004) Global phylogeography of Cassiopea (Scyphozoa: Rhizostomeae): molecular evidence for cryptic species and multiple invasions of the Hawaiian Islands. Mar. Biol. 145, 1119−1128
  17. Hooper, J. N. A. and van Soest, R. W. M. (2002) Systema Porifera. A. guide to the classification of sponges. 110pp, Kluwer Academic, New York, Boston, Dordrecht, London and Moscow
  18. Lazoski, C., Sole-Cava, A. M., Boury-Esmault, N., Klautau, M., and Russo, C. A. M. (2001) Cryptic speciation in a high gene flow scenario in the oviparous marine sponge Chondrosia reniformis. Mar. Biol. 139, 421−429
  19. Lopez, J. V., Peterson, C. L., Willoughby, R., Wright, A. E., Enright, E., et al. (2002) Characterization of genetic markers for in vitro cell line identification of the marine sponge Axinella corrugata. J. Heredity 93, 27−36
  20. Nichols, S. A. (2005) An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I. Mol. Phylogenet. Evol. 34, 81− 96
  21. Park, S. J., Choochote, W., Jitpakdi, A., Junkum, A., Kim, S. J., et al. (2003) Evidence supports conspecific relationship between morphologically and cytologically different two forms of Korean Anopheles pullus mosquitoes. Mol. Cells 16, 354− 360
  22. Posada, D. and Crandall, K. A. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817−818
  23. Schroder, H. C., Efremova, S. M., Itskovich, V. B., Celikov, S., Masuda, Y., et al. (2003) Molecular phylogeny of the freshwater sponges in Lake Baikal. J. Zool. Syst. Evol. Res. 41, 80−86
  24. Shearer, T. L., van Oppen, J. H., Romano, S. L., and Worheide, G. (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11, 2475−2487
  25. Sim, C. J. and Lee, K. J. (2003) A new species of the genus Hymeniacidon (Demospongiae: Halichondrida: Halichondriidae) from Korea. Korean J. Biol. Sci. 7, 187−189
  26. Soest, R. W. M. van (1994) Demosponge distribution patterns; in Sponges in Time and Space, van Soest, R. W. M., van Kempen, T. M. G., and Braekman, J. C. (eds.), pp. 787−815, Balkema, Rotterdam
  27. Swofford, D. L. (2003) PAUP, Phylogenetic analysis using parsimony, and other Methods, ver. 4.0. Sinauer Associates, Massachussetts
  28. Thompson, J. D., Gibson, T. J., Plewniak, D. E., Jeanmougin, F., and Higgins, D. G. (1997) The CLUSTAL X-windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis. Nucleic Acids Res. 25, 4876−4882
  29. Watkins, R. F. and Bechenbach, A. T. (1999) Partial sequence of a sponge mitochondrial genome reveals sequence similarity to Cnidaria in cytochrome oxidase subunit II and the large ribosomal RNA subunit. J. Mol. Evol. 48, 542−554
  30. Witt, J. D., Threloff, D. L., and Hebert, P. D. N. (2006) DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Mol. Ecol. 15, 3073−3082
  31. Wörheide, G., Degnanm B. M., Hooper, J. N. A., and Reitner, J. (2002a) Phylogeography and taxonomy of the Indo-Pacific reef cave dwelling coralline Demosponge Astrosclera willeyana- new data from nuclear internal transcribed spacer sequences; in Proceedings of the 9th International Coral Reef Symposium, Moosa, K, M., Soemodihardjom, S., Soegiarto, A., Romimohtarto, K., Nontji, A., et al. (eds.), pp. 339−346, Ministry for Environment, Indonesian Institute of Sciences, International Society for Reef Studies, Jakarta
  32. Worheide, G., Hooper, J. N. A., and Degnan, B. M. (2002b) Phylogeography of western Pacific Leucetta chagosenisis (Porifera: Calcarea) from DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritage Area (Australia). Mol. Ecol. 11, 1753−1768
  33. Worheide, G., Nichols, S. A., and Goldberg, J. (2004) Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies. Mol. Phylogenet. Evol. 33, 816−830