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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)

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Jellyfish Blooms: Causes, Consequences, and Recent Advances

Part of the book series: Developments in Hydrobiology ((DIHY,volume 206))

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.

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References

  • Arai, M. N., 1997. Functional biology of Scyphozoa. Chapman & Hall, New York, NY: 300.

    Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • Dawson, M. N., 2003. Macro-morphological variation among cryptic species of the moon jellyfish, Aurelia (Cnidaria: Scyphozoa). Marine Biology 143: 369–379.

    Article  Google Scholar 

  • Dawson, M. N. & D. K. Jacobs, 2001. Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin 200: 92–96.

    Article  PubMed  CAS  Google Scholar 

  • Dawson, M. N. & L. E. Martin, 2001. Geographic variation and ecological adaptation in Aurelia (Scyphozoa: Semaeosto-meae): some implications from molecular phylogenetics. Hydrobiologia 451: 259–273.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Hillis, D. M. & M. T. Dixon, 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology 66: 411–453.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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 

  • Kumar, S., K. Tamura, I. B. Jakobsen & M. Nei, 2001. MEGA3: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17: 1244–1245.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Lee, J.-S., 2000. The internally self-fertilizing hermaphroditic teleost Rivulus marmoratus (Cyprinodontiformes, Rivulidae) b-actin gene: amplification and sequence analysis with conserved primers. Marine Biotechnology 2: 161–166.

    Google Scholar 

  • Marilley, M. & P. Pasero, 1996. Common DNA structural features exhibited by eukaryotic ribosomal gene promoters. Nucleic Acids Research 24: 2204–2211.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Mayer, A. G., 1910. Medusae of the World, Vol. 3. The Scyphomedusae. Carnegie Institution of Washington, Washington, DC: 603–630.

    Google Scholar 

  • 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 

  • 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.

    Article  PubMed  Google Scholar 

  • Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406–3415.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul, 133-791, South Korea

    Jang-Seu Ki

  2. Polar BioCenter, Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, South Korea

    Il-Chan Kim

  3. Department of Chemistry, and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul, 133-791, South Korea

    Jae-Seong Lee

Authors
  1. Jang-Seu Ki
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  2. Il-Chan Kim
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  3. Jae-Seong Lee
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Editor information

Editors and Affiliations

  1. Australian Rivers Institute and Griffith School of Environment, Griffith University, Australia

    Kylie A. Pitt

  2. Shannon Point Marine Center, Western Washington University, Washington, USA

    Jennifer E. Purcell

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Ki, JS., Kim, IC., Lee, JS. (2008). 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). In: Pitt, K.A., Purcell, J.E. (eds) Jellyfish Blooms: Causes, Consequences, and Recent Advances. Developments in Hydrobiology, vol 206. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9749-2_15

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