• dinoflagellate;
  • ITS2;
  • ribosomal;
  • secondary structure;
  • Symbiodinium

Internal transcribed spacer (ITS) regions of the eukaryotic rDNA operon are integral to the correct processing and maturation of rRNAs. To further understand the evolution of this region, we elucidated the secondary structure of ITS2 from representatives of the eight divergent clades of Symbiodinium Freud., a large genus of dinoflagellate endosymbionts occurring in association with zooxanthellate marine protists and invertebrates. Symbiodinium ITS2 molecules folded into one of two distinct conformations. One conformation, the “four-fingered hand” model, has been described from a wide variety of eukaryotes, including free-living dinoflagellates. A monophyletic assemblage comprising several Symbiodinium clades shared an unusual conformation, a five-stem model previously known only from drosopholids, indicating that it arose in the common ancestor to this “superclade” of Symbiodinium. Several conserved features were identified in the ITS2 secondary structures, including a pyrimidine–pyrimidine bulge and a highly conserved 11 bp sequence motif, that correspond to known processing sites in other eukaryotes. Lastly, the ITS2 structural data are discussed in the context of Symbiodinium evolution, phylogenetics, and ecology.