Advertisement

Hydrobiologia

, Volume 616, Issue 1, pp 229–239 | Cite as

Comparative analysis of nuclear ribosomal DNA from the moon jelly Aurelia sp.1 (Cnidaria: Scyphozoa) with characterizations of the 18S, 28S genes, and the intergenic spacer (IGS)

  • Jang-Seu Ki
  • Il-Chan Kim
  • Jae-Seong Lee
JELLYFISH BLOOMS

Abstract

Nuclear ribosomal DNAs (rDNA) constitute a multi-gene family with tandemly arranged units linked by an intergenic spacer (IGS). Here we present the complete DNA sequence (7,731 bp) of a single repeat unit of an rDNA sequence from the moon jelly Aurelia sp.1 (Cnidaria: Scypozoa). The tandemly repeated rDNA units consisted of coding and non-coding regions, whose arrangement was 18S rDNA (1,814 bp, 46.2% of GC content)-internal transcribed spacer 1 (ITS1: 272 bp, 39.7%)-5.8S rDNA (158 bp; 50.7%)-ITS2 (278 bp, 51.4%)-28S rDNA (3,606 bp, 49.7%)-IGS (1,603 bp, 45.6%). GC composition in the single unit of rDNA was 47.8%. None of the 5S rDNA was found in the repeat units. Putative structures of a termination transcription signal (poly(T) tract) and promoter-like bi-repeats within the non-coding region were also identified. A block of minisatellites with five repeats was detected within the IGS. Comparative analyses of parsimony and dot plots showed that the IGS was highly informative. The sequence revealed here was the first completion of rDNA from the phylum Cnidaria, using as a model of rDNA for making molecular comparisons of jellyfish members.

Keywords

Jellyfish Nuclear rDNA Transcription repeat unit Minisatellite 

Notes

Acknowledgments

We would like to thank Drs. Sheikh Raisuddin and Hans-Uwe Dahms for English editing on the manuscript. We are very grateful to Dr. Timothy J. Page and two anonymous reviewers for reading and critical comments. This work was supported by grants of KOSEF NRL (2006) and ETEP (2006) funded to Jae-Seong Lee, and by a grant of KOSEF (2007) funded to Heum Gi Park. Thus work was also supported by a grant from Korea Polar Research Institute (PE08050) funded to Il-Chan Kim.

References

  1. Arai, M. N., 1997. Functional biology of Scyphozoa. Chapman & Hall, New York, NY: 300.Google Scholar
  2. Chen, C. A., D. J. Miller, N. V. Wei, C.-F. Dai & H.-P. Yang, 2000. The ETS/IGS region in a lower animal, the seawhip, Junceella fragilis (Cnidaria: Anthozoa: Octocorallia): compactness, low variation and apparent conservation of a pre-rRNA processing signal with fungi. Zoological Studies 39: 138–143.Google Scholar
  3. Collins, A. G., P. Schuchert, A. C. Marques, T. Jankowski, M. Medina & B. Schierwater, 2006. Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Systematic Biology 55: 97–115.PubMedCrossRefGoogle Scholar
  4. Dawson, M. N., 2003. Macro-morphological variation among cryptic species of the moon jellyfish, Aurelia (Cnidaria: Scyphozoa). Marine Biology 143: 369–379.CrossRefGoogle Scholar
  5. Dawson, M. N. & D. K. Jacobs, 2001. Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin 200: 92–96.PubMedCrossRefGoogle Scholar
  6. Dawson, M. N. & L. E. Martin, 2001. Geographic variation and ecological adaptation in Aurelia (Scyphozoa: Semaeostomeae): some implications from molecular phylogenetics. Hydrobiologia 451: 259–273.CrossRefGoogle Scholar
  7. Dawson, M. N., A. Sen Gupta & M. H. England, 2005. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species. Proceedings of the National Academy of Sciences of the United States of America 102: 11968–11973.PubMedCrossRefGoogle Scholar
  8. Drouin, G., J. D. Hofman & W. F. Doolittle, 1987. Unusual ribosomal RNA gene organization in copepods of the genus Calanus. Journal of Molecular Biology 196: 943–946.PubMedCrossRefGoogle Scholar
  9. Hassouna, N., B. Michot & J.-P. Bachellerie, 1984. The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Research 12: 3563–3583.PubMedCrossRefGoogle Scholar
  10. Hillis, D. M. & M. T. Dixon, 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology 66: 411–453.PubMedCrossRefGoogle Scholar
  11. Jeong, S. W., W. H. Lang & R. H. Reeder, 1995. The release element of the yeast polymerase I transcription terminator can function independently of Reb1p. Molecular and Cellular Biology 15: 5929–5936.PubMedGoogle Scholar
  12. Ki, J.-S. & M.-S. Han, 2007. Informative characteristics of 12 divergent domains in complete large subunit rDNA sequences from the harmful dinoflagellate genus, Alexandrium (Dinophyceae). Journal of Eukaryotic Microbiology 54: 210–219.PubMedCrossRefGoogle Scholar
  13. Ki, J.-S., D.-S. Hwang, K. Shin, W. D. Yoon, D. Lim, Y. S. Kang, Y. Lee & J. -S. Lee, 2008. Recent moon jelly (Aurelia sp.1) blooms in Korean coastal waters suggest global expansion: examples inferred from mitochondrial COI and nuclear ITS–5.8S rDNA sequences. ICES Journal of Marine Science 65: 443–452.CrossRefGoogle Scholar
  14. Kimura, M., 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111–120.PubMedCrossRefGoogle Scholar
  15. Kramp, P. L., 1961. Synopsis of the medusae of the world. Journal of the Marine Biological Association of the United Kingdom 40: 337–342.Google Scholar
  16. Kumar, S., K. Tamura, I. B. Jakobsen & M. Nei, 2001. MEGA3: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17: 1244–1245.PubMedCrossRefGoogle Scholar
  17. Lang, W. H., B. E. Morrow, Q. Ju, J. R. Warner & R. H. Reeder, 1994. A model for transcription termination by RNA polymerase I. Cell 79: 527–534.PubMedCrossRefGoogle Scholar
  18. Lee, J.-S., 2000. The internally self-fertilizing hermaphroditic teleost Rivulus marmoratus (Cyprinodontiformes, Rivulidae) β-actin gene: amplification and sequence analysis with conserved primers. Marine Biotechnology 2: 161–166.PubMedGoogle Scholar
  19. Marilley, M. & P. Pasero, 1996. Common DNA structural features exhibited by eukaryotic ribosomal gene promoters. Nucleic Acids Research 24: 2204–2211.PubMedCrossRefGoogle Scholar
  20. Mason, S., M. Wallisch & I. Grummt, 1997. RNA polymerase I transcription termination: similar mechanisms are employed by yeast and mammals. Journal of Molecular Biology 268: 229–234.PubMedCrossRefGoogle Scholar
  21. Mathews, D. H., J. Sabina, M. Zuker & D. H. Turner, 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology 288: 911–940.PubMedCrossRefGoogle Scholar
  22. Mayer, A. G., 1910. Medusae of the World, Vol. 3. The Scyphomedusae. Carnegie Institution of Washington, Washington, DC: 603–630.Google Scholar
  23. Schlötterer, C., 1998. Ribosomal DNA probes and primers. In Karp, A., P. G. Isaac & D. S. Ingram (eds), Molecular Tools for Screening Biodiversity. Chapman & Hall, London: 267–276.Google Scholar
  24. Schroth, W., G. Jarms, B. Streit & B. Schierwater, 2002. Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp. BMC Evolutionary Biology 2: 1–10.PubMedCrossRefGoogle Scholar
  25. Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406–3415.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Department of Molecular and Environmental Bioscience, Graduate SchoolHanyang UniversitySeoulSouth Korea
  2. 2.Polar BioCenter, Korea Polar Research InstituteKorea Ocean Research and Development InstituteIncheonSouth Korea
  3. 3.Department of Chemistry, and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural SciencesHanyang UniversitySeoulSouth Korea

Personalised recommendations