Published online 13 January 2004
Nucleic Acids Research, 2004, Vol. 32, No. 1 307-315
© 2004 Oxford University Press
Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates
Freie Universität Berlin, Institut für Geologische Wissenschaften–Fachrichtung Paläontologie, Malteserstraße 74–100, D-12249 Berlin, Germany and 1 Humboldt Universität Berlin, Museum für Naturkunde, Institut für Systematische Zoologie, Invalidenstraße 43, D-10015 Berlin, Germany
*To whom correspondence should be addressed. Tel: +49 30 838 70 808; Fax: +49 30 838 70 245; Email: caix{at}zedat.fu-berlin.de
+AY327462, AY427463
Secondary structure models of the 5.8S rRNA and both internal transcribed spacers (ITS1 and ITS2) are proposed for Calciodinelloideae (Peridiniaceae) and are also plausible for other dinoflagellates. The secondary structure of the 5.8S rRNA corresponds to previously developed models, with two internal paired regions and at least one 5.8S rRNA–28S rRNA interaction. A general secondary structure model of ITS1 for Calciodinelloideae (and other dinoflagellates), consisting of an open multibranch loop with three major helices, is proposed. The homology of these paired regions with those found in other taxa, published in previous studies (e.g. yeast, green algae and Platyhelmithes) remains to be determined. Finally, a general secondary structure model of ITS2 for Calciodinelloideae (and other dinoflagellates) is reconstructed. Based on the 5.8S rRNA–28S rRNA interaction, it consists of a closed multibranch loop, with four major helices. At least helix III and IV have homology with paired regions found in other eukaryotic taxa (e.g. yeast, green algae and vertebrates). Since the secondary structures of both ITS regions are more conserved than the nucleotide sequences, their analysis helps in understanding molecular evolution and increases the number of structural characters. Thus, the structure models developed in this study may be generally useful for future phylogenetic analyses.
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