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

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