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To identify fast-evolving genes in reef-building corals, we performed direct comparative sequence analysis with expressed sequence tag (EST) datasets from two acroporid species:  Acropora palmata  from the Caribbean Sea and  A. millepora  from the Great Barrier Reef in Australia. Comparison of 589 independent sequences from 1,421  A. palmata  contigs, with 10,247  A. millepora  contigs resulted in the identification of 196 putative homologues. Most of the homologous pairs demonstrated high amino acid similarities (over 90%). Comparisons of putative homologues showing low amino acid similarities (under 90%) among the  Acropora  species to the near complete datasets from two other cnidarians ( Hydra magnipapillata  and  Nematostella vectensis ) implied that some were non-orthologous. Within 86 homologous pairs, 39 exhibited dN/dS ratios significantly less than 1, suggesting that these genes are under purifying selection associated with functional constraints. Eight independent genes showed dN/dS ratios exceeding 1, while three deviated significantly from 1, suggesting that these genes may play important roles in the adaptive evolution of  Acropora . Our results also indicated that CEL-III lectin was under positive selection, consistent with a possible role in immunity or symbiont recognition. Further studies are needed to clarify the possible functions of the genes under positive selection to provide insight into the evolutionary process of corals.

Identification of Fast-Evolving Genes in the Scleractinian Coral Acropora Using Comparative EST Analysis