Zoological Studies

Vol. 43 No. 4, 2004

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

Chaolun Allen Chen1,2,*, Chau-Ching Chang1,2, Nuwei Vivian Wei1,2, Chien-Hsun Chen1,2, Yi-Ting Lein1, Ho-E Lin1, Chang-Feng Dai2 and Carden C. Wallace3

1Research Center for Biodiversity, Academia Sinica, Nankang, Taipei, Taiwan 115
2Institute of Oceanography, National Taiwan University, Taipei, Taiwan 106
3Museum of North Queensland, Townsville, Queensland Q4810, Australia

Chaolun Allen Chen, Chau-Ching Chang, Nuwei Vivian Wei, Chien-Hsun Chen, Yi-Ting Lein, Ho-E Lin, Chang-Feng Dai and Carden C. Wallace (2004) 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 shorter 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 using ITS2 data produced a concordant tree to those based on mitochondrial and nuclear genes. The comparative analysis indicated that the extremely high ITS intragenomic divergence of Acropora is an exception rather than the rule for the evolutionary history of scleractinian corals. Despite the atypical and unusual pattern of molecular evolution in the genus Acropora, data of the ITS2 are still applicable, with adequate adjustment of secondary structures, to the primary sequence alignment of different levels of phylogenetic analyses, from populations to genera, in scleractinian corals.

Key words: Internal transcribed spacer 2, Secondary structure, Conserved domain, Scleractinian corals, Phylogenetic utility.

*Correspondence: Tel: 886-2-27899549. Fax: 886-2-27858059. E-mail: cac@gate.sinica.edu.tw