Secondary Structure and Phylogenetic Utility of the Ribosomal Internal Transcribed Spacer 2 (ITS2) in Scleractinian Corals

Chang-Feng Dai and Carden C. Wallace (2004) Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals. Zoological Studies 43(4): 759-771. In this study, we examined the nucleotide characteristics, the secondary structure, and phylogenetic utility of the ribosomal internal spacer 2 (ITS2) from 54 species of scleractinian corals, representing 25 genera and 11 families of both the complex and robust clades previously defined through molecular phylogenetic analyses. The lengths and nucleotide contents of the ITS2 were highly variable among corals. The ITS2 of Acropora is significantly short-er than those of other corals. Dinucleotide or tetranucleotide microsatellites were identified in the genera Acropora, Cyphastrea, Favites, Goniastrea, Hydnophora, Montipora, Madracis, and Porites. Three distinct types of secondary structures with the smallest free energy values were predicted using the computer software, Mfold. A standard 4 domains were observed in 17 species of corals, while 23 species has a modified 5 domains with domain I divided into 2 subdomains. These 2 types of secondary structures were observed across 11 coral families. The 3rd type, 5 domains with domain III divided into 2 subdomains, was only seen in the genus Acropora. Among the domains, domain II is highly conserved and is flanked by conserved sequence motifs in adjacent stems. The motif, 5-CRCGGYC-3, and its compensatory bases were highly conserved in both the complex and robust clades of scleractinian corals. The robust-clade phylogeny constructed usin