ALGAE

The Korean Society of Phycology (한국조류학회(藻類))
권호 표지
DOI QR코드

DOI QR Code

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
Download PDF
⟨ Previous Next ⟩

Abstract

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.

Keywords

References

  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 https://doi.org/10.1016/j.ympev.2007.03.024
  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 https://doi.org/10.1139/b88-151
  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 https://doi.org/10.1080/09670260500050026
  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 https://doi.org/10.1080/09670260601044068
  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 https://doi.org/10.1127/0029-5035/2007/0085-0331
  6. Guiry M.D. and Guiry G.M. (2009). “Stephanodiscus”. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. http://www.algaebase.org/. 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 https://doi.org/10.1023/A:1015610900467
  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 https://doi.org/10.1093/nar/12.8.3563
  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 https://doi.org/10.1080/0269249X.2004.9705871
  12. Huelsenbeck J.P. and Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755 https://doi.org/10.1093/bioinformatics/17.8.754
  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 https://doi.org/10.1111/j.1529-8817.2006.00161.x
  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 https://doi.org/10.1007/s00300-005-0078-1
  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 https://doi.org/10.1007/s00300-008-0514-0
  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 https://doi.org/10.1007/s10811-005-7211-y
  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 https://doi.org/10.1111/j.1550-7408.2007.00251.x
  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 https://doi.org/10.1007/BF02106180
  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 https://doi.org/10.1186/1746-1448-4-17
  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 https://doi.org/10.1093/molbev/msm092
  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 https://doi.org/10.1093/nar/22.22.4673
  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 https://doi.org/10.1080/0269249X.2002.9705561

Cited by

  1. Morphological and genetic variability of assemblages ofCyclotella ocellataPantocsek/C. comensisGrunow complex (Bacillariophyta, Thalassiosirales) vol.30, pp.4, 2015, https://doi.org/10.1080/0269249X.2015.1101402
  2. Pantocsekiella, a new centric diatom genus based on morphological and genetic studies vol.16, pp.1, 2016, https://doi.org/10.5507/fot.2015.028
  3. Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms vol.50, 2013, https://doi.org/10.1016/j.bse.2013.03.025
  4. Nuclear rDNA characteristics for DNA taxonomy of the centric diatom Chaetoceros (Bacillariophyceae) vol.25, pp.2, 2010, https://doi.org/10.4490/algae.2010.25.2.065
  5. Checklist of the Pacific marine macroalgae of Central America vol.54, pp.1, 2011, https://doi.org/10.1515/bot.2011.001