Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms

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 Kutzing ex de Brebisson, Discostella Houk 8.2 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. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.This work was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2011-0027480), by the “Polar Academic Program (PAP)” of the Korea Polar Research Institute (KOPRI) funded to Jang-Seu Ki, and by a grant from Marine Biotechnology Program funded by Ministry of Land, Transport and Maritime Affairs of Korean Government