Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms |
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| Affiliation: | 1. Department of Geography, Environmental Change Research Centre, University College London, Gower Street, London WC1E 6BT, UK;2. Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan 420000, Russian Federation;3. School of Geography, Archaeology and Palaeoecology, Queen''s University Belfast, BT7 1 NN Northern Ireland, UK;4. Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK;5. School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden;6. Faculty of Mathematics and Natural Sciences, Quaternary Geology, University of Cologne, Albertus_Magnus-Platz, 50923 Köln, Germany;7. Kamchatka Research Institute of Fisheries and Oceanography, Petropavlovsk-Kamchatski, Russian Federation;8. Quaternary Sciences, Departrment of Geology, Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden;1. Department of Ecology and Evolutionary Biology and Museum of Natural History, University of Colorado, Boulder, Colorado, USA.;2. University of Michigan Biological Station, Pellston, Michigan, USA.;3. Department of Integrative Biology, and Texas Memorial Museum, University of Texas at Austin, Austin, Texas, USA.;4. Life Sciences Department, Natural History Museum, London, United Kingdom.;5. Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, USA.;6. Center for Great Lakes and Aquatic Sciences, University of Michigan, Ann Arbor, Michigan, USA.;7. Center for Water and the Environment, Natural Resources Research Institute, University of Minnesota Duluth, Ely, Minnesota, USA |
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| Abstract: | Diatoms are highly diversified microeukaryotes with a taxonomy that has been under perpetual revision, particularly by means of molecular analyses. In this study, we evaluated typical genes to find the best molecular marker for the DNA taxonomy of centric diatoms, including Chaetoceros Ehrenberg, Cyclotella Kützing ex de Brébisson, Discostella Houk & Klee, Stephanodiscus Ehrenberg, and Thalassiosira Cleve. Our test genes included nuclear ribosomal RNA (e.g. small subunit, 5.8S, and large subunit [LSU]), and chloroplast genes (e.g. ribulose-1, 5-biphoshate carboxylase oxygenase and D1 protein of the photosystem II reaction centre core complex [psbA]). Calculated genetic divergence was highest for LSU ribosomal RNA D1-D5 (p-distance of 12.3), followed by 5.8S (7.7), ribulose-1, 5-biphoshate carboxylase oxygenase (7.4), small subunit (6.6), and psbA (3.7). The phylogenetic trees for individual genes effectively separated taxonomically tested centric diatoms with different phylogenetic resolutions; however, psbA was incongruent with others. These taxonomic resolving powers were in agreement with genetic divergences. Parsimony analysis showed that LSU evolved 1.97 times more rapidly than psbA and 1.07 times more rapidly than 5.8S. These results suggest that all of the tested genes except psbA can be used as taxonomic markers for centric diatoms and that LSU is the best molecular marker. |
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| Keywords: | Diatom Divergence Molecular taxonomy rRNA Chloroplast gene |
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