Title
Secondary Structure Models for the Internal Transcribed Spacer (ITS) Region 1 from Symbiotic Dinoflagellates
Document Type
Article
Publication Date
7-2010
Abstract
Ribosomal genes and their spacers have been extensively utilized to examine the biodiversity and phylogenetics of protists. Among these, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) are known to form secondary structures that are critically important for proper processing of the pre-rRNA into mature ribosomes. Although the secondary structure of ITS2 has been widely investigated, considerably less is known about ITS1 and its secondary structure. Here, secondary structures of the ITS1 were modeled for 46 ITS “types” from Symbiodinium, a diverse dinoflagellate genus that forms symbioses with many protists and metazoans, using comparative phylogenetic and minimum free energy approaches. The predicted ITS1 secondary structures for each Symbiodinium “type” were highly stable (ΔG=−46.40 to −85.30 kcal mol−1 at 37 °C) and consisted of an open loop with five helices separated by single-stranded regions. Several structural characteristics were conserved within monophyletic sub-groups, providing additional support for the predicted structures and the relationships within this genus. Finally, the structures were applied to identify potential pseudogenes from five Symbiodinium ITS1 datasets. Consequently, ITS1 secondary structures are useful in understanding the biology and phylogenetics, as well as recognizing and excluding questionable sequences from datasets, of protists such as Symbiodinium.
Recommended Citation
Thornhill, DJ, JB Lord (2010) Secondary Structure Models for the Internal Transcribed Spacer (Its) Region 1 from Symbiotic Dinoflagellates. Protist 161 3: 434-51 doi:10.1016/j.protis.2009.11.004
Comments
Jenna B. Lord was a Bowdoin student when this research was conducted.