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Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis.

Iguchi A, Shinzato C, Forêt S, Miller DJ - PLoS ONE (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan. iguchi.a0218@gmail.com

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.

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Distribution of the number of amino acid similarities in 98 Acropora millepora–A. palmata homologous pairs.
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pone-0020140-g001: Distribution of the number of amino acid similarities in 98 Acropora millepora–A. palmata homologous pairs.

Mentions: Of the 589 A. palmata contigs matching only unknown or unnamed proteins, hypothetical ones or with no significant non-cnidarian matches in the databases, 196 had putative orthologs in A. millepora. The amino acid similarities of 98 gene pairs for which correct translation positions were available (longer translation) were examined. The amino acid similarities among these homologous pairs ranged from 33.6% to 100% (average 89.5%; Fig. 1), with 74 and 24 sequences demonstrating greater than and less than 90% similarity, respectively (Fig. 1). Sequences giving low amino acid similarities between Acropora species were subjected to BLAST analysis performed against the EST datasets of Hydra magnipapillata and Nematostella vectensis. Several of the 13 A. palmata matching only unknown, unnamed, or hypothetical proteins and with <90% amino acid similarity with A. millepora were found to have better matches in H. magnipapillata and N. vectensis than in A. millepora and were hence excluded from further consideration (Table 1; <76.8% amino acid similarities in A. millepora).


Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis.

Iguchi A, Shinzato C, Forêt S, Miller DJ - PLoS ONE (2011)

Distribution of the number of amino acid similarities in 98 Acropora millepora–A. palmata homologous pairs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3119059&req=5

pone-0020140-g001: Distribution of the number of amino acid similarities in 98 Acropora millepora–A. palmata homologous pairs.
Mentions: Of the 589 A. palmata contigs matching only unknown or unnamed proteins, hypothetical ones or with no significant non-cnidarian matches in the databases, 196 had putative orthologs in A. millepora. The amino acid similarities of 98 gene pairs for which correct translation positions were available (longer translation) were examined. The amino acid similarities among these homologous pairs ranged from 33.6% to 100% (average 89.5%; Fig. 1), with 74 and 24 sequences demonstrating greater than and less than 90% similarity, respectively (Fig. 1). Sequences giving low amino acid similarities between Acropora species were subjected to BLAST analysis performed against the EST datasets of Hydra magnipapillata and Nematostella vectensis. Several of the 13 A. palmata matching only unknown, unnamed, or hypothetical proteins and with <90% amino acid similarity with A. millepora were found to have better matches in H. magnipapillata and N. vectensis than in A. millepora and were hence excluded from further consideration (Table 1; <76.8% amino acid similarities in A. millepora).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan. iguchi.a0218@gmail.com

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.

Show MeSH