4.0 Article

An Evaluation of the Use of the LSU rRNA D1-D5 Domain for DNA-based Taxonomy of Eukaryotic Protists

Journal

PROTIST
Volume 161, Issue 3, Pages 342-352

Publisher

ELSEVIER GMBH
DOI: 10.1016/j.protis.2010.01.003

Keywords

Eukaryotes; protists; heterotrophic flagellates; DNA-taxonomy; ribosomal genes; D1-D5 domain of LSU rRNA; groundwater

Categories

Funding

  1. German Research Foundation (DFG) [Ar 288/7, Ta 99/21]
  2. The Russian Foundation of Basic Research (RFBR) [08-04-00244]

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Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a widerange of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from ground water. (C) 2010 Elsevier GmbH. All rights reserved.

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