STRUCTURE AND EVOLUTION OF THE RDNA INTERNAL TRANSCRIBED SPACER (ITS) REGION 2 IN THE SYMBIOTIC DINOFLAGELLATES (SYMBIODINIUM, DINOPHYTA)¹

Abstract

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 freeliving 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.

Changes in coral microbial communities in response to a natural pH gradient

“…In contrast, B. europaea contained Symbiodinium B2 mixed with a novel Symbiodinium that was 95% similar to 'Mediterranean A' (Visram et al, 2006;Hunter et al, 2007). Symbiodinium densities (cells per polyp) did not vary between the sites in both corals (one-way ANOVA, P40.05).…”

Character lability in deep-sea bamboo corals (Octocorallia, Isididae, Keratoisidinae)

“…One of the many reasons why secondary structures from RNA molecules are useful in systematics is because they are relatively well-conserved structures among eukaryotes (Hunter et al 2007, Coleman & van Oppen 2008. Based on the conspicuous homologies, secondary structures facilitate the correct alignment of gene sequences that exhibit a great deal of indels, such as ITS2 (Aguilar & Sánchez 2007).…”

Specificity in communities of Symbiodinium in corals from Johnston Atoll

“…The remaining clone singletons were assumed to be artifacts or rare intragenomic repeats not useful for diversity analysis, and the nucleotide at the site of polymorphism converted to the consensus. In addition, IT2S folding was conducted using previously published Symbiodinium ITS2 structures as templates (Hunter et al 2007, Thornhill et al 2007) in the ITS2 database interactive website , Selig et al 2008) and manually edited using the software 4SALE (Seibel et al , 2008. Potential pseudogenes were characterized by significant changes to the 5.8S sequence not observed in Symbiodinium or other closely related dinoflagellates (Thornhill et al 2007) and changes to the secondary structure of the ITS2 RNA molecule that likely disrupt the functional fold.…”