Abstract
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.
Highlights
One of the main aims of evolutionary biology is to understand the genetic basis of adaptive change [1,2]
Sequences giving low amino acid similarities between Acropora species were subjected to BLAST analysis performed against the expressed sequence tag (EST) datasets of Hydra magnipapillata and Nematostella vectensis
To examine the possibility that some of the sequence pairs with,90% amino acid similarity between the two were not orthologous, the Acropora sequences were subjected to BLAST analyses against the EST datasets of Hydra magnipapillata and Nematostella vectensis
Summary
One of the main aims of evolutionary biology is to understand the genetic basis of adaptive change [1,2]. Genes associated with adaptive evolution often show relatively high rates of evolutionary change and are under selection [3,4]. The identification of fast-evolving genes can contribute to the understanding of the genetic bases of adaptive evolution, and provide insights into ecological niche partitioning and phenomena involved in the co-evolutionary race. The identification of molecules involved in symbiosis and pathogen recognition are likely to be fundamental importance in terms of understanding the genetic bases of coral bleaching and diseases which are the threats to the survival of corals [16]. Given that in the other animals the molecules involved in these processes are under positive selection, fast-evolving genes are good targets to uncover the molecular mechanisms of these phenomena in corals
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