Comparative Molecular Analysis of Freshwater Centric Diatoms with Particular Emphasis on the Nuclear Ribosomal DNA of Stephanodiscus (Bacillariophyceae)

  • Ki, Jang-Seu (Department of Life Science, College of Natural Sciences, Sangmyung University)
  • Published : 2009.09.01


DNA-based discrimination of species is a powerful way for morphologically otherwise similar species, like centric diatoms. Here, the author sequenced long-range nuclear ribosomal DNAs, spanning from the 18S to the D5 region of the 28S rDNA, of Stephanodiscus, particularly including a Korean isolate. By comparisons, high DNA similarities were detected from the rDNAs of nine Stephanodiscus (>99.4% in 18S rDNA, >98.0% in 28S rDNA). Their genetic distances, however, were significantly different (Kruskal-Wallis test, p < 0.01) compared to two related genera, namely Cyclotella and Discostella. In addition, genetic distances of 18S rDNAs were significantly different (Student’s t-test, p = 0.000) against those of the 28S rDNAs according to individual genera (Cyclotella, Discostella, and Stephanodiscus). Phylogenetic analyses showed that Stephanodiscus and Discostella showed a sister taxon relationship, and their clade was separated from a cluster of Cyclotella (1.00 PP, 100% BP). This suggests that Stephanodiscus has highly conserved sequences of both 18S and 28S rDNA; however, Stephanodiscus is well-separated from other freshwater centric diatoms, such as Cyclotella and Discostella, at the generic level.


  1. Alverson A.J., Jansen R.K. and Theriot E.C. 2007. Bridging the Rubicon: phylogenetic analysis reveals repeated colonization of marine and fresh waters by thalassiosiroid diatoms. Mol. Phylogenet. Evol. 45: 193-210
  2. Beakes G., Canter H.M. and Jaworski G.H.M. 1988. Zoospore ultrastructure of Zygorhizidium affluens Canter and Z. planktonicum Canter, two chytrids parasitizing the diatom Asterionella formosa Hassall. Can. J. Bot. 66: 1054-1067
  3. Beszteri B., Acs E. and Medlin L.K. 2005. Conventional and geometric morphometric studies of valve ultrastructural variation in two closely related Cyclotella species (Bacillariophyceae). Eur. J. Phycol. 40: 89-103
  4. Beszteri B., John U. and Medlin L.K. 2007. An assessment of cryptic genetic diversity within the Cyclotella meneghiniana species complex (Bacillariophyta) based on nuclear and plastid genes, and amplified fragment length polymorphisms. Eur. J. Phycol. 42: 47-60
  5. Bruder K. and Medlin L.K. 2007. Molecular assessment of phylogenetic relationships in selected species/genera in the Naviculoid diatoms (Bacillariophyta). I. The genus Placoneis. Nova Hedwigia 85: 331-352
  6. Guiry M.D. and Guiry G.M. (2009). “Stephanodiscus”. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. Retrieved on 2009-08-15
  7. Ha K., Jang M.H. and Joo G.J. 2002. Spatial and temporal dynamics of phytoplankton communities along a regulated river system, the Nakdong River, Korea. Hydrobiologia 470: 235-245
  8. Hall T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41: 95-98
  9. Han M.-S., Lee H.R., Hong S.S., Kim Y.O., Lee K., Choi Y.K., Kim S. and Yoo K.I. 2002. Ecological studies on Togyo reservoir system in Chulwon, Korea. V. Seasonal changes of size-fractionated standing crops and chlorophyll a of phytoplankton in Kyungan Stream of Pal'tang Reservoir, Korea. Korean J. Environ. Biol. 20: 91-99
  10. Hassouna N., Michot B. and Bachellerie J.-P. 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 Res. 12: 3563-3583
  11. Houk V. and Klee R. 2004. The stelligeroid taxa of the genus Cyclotella (Kützing) Brebisson (Bacillariophyceae) and their transfer into the new genus Discostella gen. nov. Diatom Res. 19: 203-28
  12. Huelsenbeck J.P. and Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755
  13. Jung S.W., Han M.-S. and Ki J.-S. 2009. Molecular genetic divergence of the centric diatom Cyclotella and Discostella (Bacillariophyceae) revealed by nuclear ribosomal DNA comparisons. J. Appl. Phycol. DOI 10.1007/s10811-009-9462-5
  14. Kaczmarska I., Beaton M., Benoit A.C. and Medlin L.K. 2005. Molecular phylogeny of selected members of the order Thalassiosirales (Bacillariophyta) and evolution of the Fultoportula. J. Phycol. 42: 121-138
  15. Karsten U., Schumann R., Rothe S., Jung I. and Medlin L. 2006. Temperature and light requirements for growth of two diatom species (Bacillariophyceae) isolated from an Arctic macroalga, Polar Biol. 29: 476-486
  16. Ki J.-S., Cho S.-Y., Katano T., Jung S.W., Lee J., Park B.S., Kang S.-H. and Han M.-S. 2009. Comprehensive comparisons of three pennate diatoms, Diatoma tenuae, Fragilaria vaucheriae, and Navicula pelliculosa, isolated from summer Arctic reservoirs (Svalbard 79${^{\circ}}$N), by fine-scale morphology and nuclear 18S ribosomal DNA. Polar Biol. 32: 147-159
  17. Ki J.-S. and Han M.-S. 2005. Sequence-based diagnostics and phylogenetic approach of uncultured freshwater dinoflagellate Peridinium species based on single-cell sequencing of rDNA. J. Appl. Phycol. 17: 147-153
  18. Ki J.-S. and Han, M.-S. 2007. Informative characteristics of 12 divergent domains in complete large subunit rDNA sequences from the harmful dinoflagellate genus, Alexandrium (Dinophyceae). J. Eukaryotic Microbiol. 54: 210-219
  19. Kim M.-C., La G.-H., Kim. H.-W., Jeong K.-S., Kim D.-K. and Joo G.-J. 2008. The effect of water temperature on proliferation of Stephanodiscus sp. in vitro from the Nakdong River, South Korea. Korean J. Limnol. 41: 26-33
  20. Kim Y.J. 1998. Ecological characteristics of phytoplankton community in lake Paltang Dam. Korean J. Limnol. 31: 225-234
  21. Lenaers G., Maroteaux L., Michot B. and Herzog M. 1989. Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA. J. Mol. Evol. 29: 40-51
  22. Nylander J.A.A. 2004. MrModeltest v2 (Evolutionary Biology Centre, Uppsala Univ, Uppsala, Sweden
  23. Oliva M.G., Lugo A., Alcocer J. and Cantoral-Uriza E.A. 2008. Morphological study of Cyclotella choctawhatcheeana Prasad (Stephanodiscaceae) from a saline Mexican lake. Saline Syst. 4: 17
  24. Page R.D.M. 1996. TREEVIEW: an application to display of phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357-358
  25. Tamura K., Dudley J., Nei M. and Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599
  26. Thompson J.D., Higgins D.G. and Gibbson T.J. 1997. Clustal X: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673
  27. Wolf M., Scheffler W. and Nicklisch A. 2002. Stephanodiscus neoastraea and Stephanodiscus heterostylus (Bacillariophyta) are one and the same species. Diatom Res. 17: 445-451

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