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Rapid evolution of coral proteins responsible for interaction with the environment.

Voolstra CR, Sunagawa S, Matz MV, Bayer T, Aranda M, Buschiazzo E, Desalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M - PLoS ONE (2011)

Bottom Line: Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla.The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception.This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.

View Article: PubMed Central - PubMed

Affiliation: Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. christian.voolstra@kaust.edu.sa

ABSTRACT

Background: Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably.

Methodology/principal findings: We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experience adaptive evolution. 7% of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium.

Conclusion/relevance: This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.

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Related in: MedlinePlus

Detection of molecular functions experiencing accelerated protein sequence evolution.The dendrogram reflects the proportion of orthologs shared between different categories in our dataset (see Material and Methods). The colors of the corresponding cells and the overlying trace line represent P-values of Mann-Whitney U test for elevated dS, dN, and dN/dS values. The first transition to the darker color signifies P<0.05 in an individual comparison. The dashed orange line indicates the 10% false discovery rate cutoff.
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pone-0020392-g003: Detection of molecular functions experiencing accelerated protein sequence evolution.The dendrogram reflects the proportion of orthologs shared between different categories in our dataset (see Material and Methods). The colors of the corresponding cells and the overlying trace line represent P-values of Mann-Whitney U test for elevated dS, dN, and dN/dS values. The first transition to the darker color signifies P<0.05 in an individual comparison. The dashed orange line indicates the 10% false discovery rate cutoff.

Mentions: We applied Mann-Whitney U (MWU) test to see whether the indices of evolutionary rates were distributed unevenly across functional categories, based on annotations established using Gene Ontology (GO) terms for “biological process” and “molecular function”. Plotting the MWU test P-values across GO categories (Figures 2 and 3, Figures S2 and S3) indicated that the observed dN/dS variation is predominantly driven by variation in dN rates (as expected under varying selection pressures). We visualized a number of functional clusters showing a tendency to rank higher than the rest of the dataset with respect to dN/dS. Several of the highlighted GO categories passed the 10% false discovery rate cutoff [40] (Table 3).


Rapid evolution of coral proteins responsible for interaction with the environment.

Voolstra CR, Sunagawa S, Matz MV, Bayer T, Aranda M, Buschiazzo E, Desalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M - PLoS ONE (2011)

Detection of molecular functions experiencing accelerated protein sequence evolution.The dendrogram reflects the proportion of orthologs shared between different categories in our dataset (see Material and Methods). The colors of the corresponding cells and the overlying trace line represent P-values of Mann-Whitney U test for elevated dS, dN, and dN/dS values. The first transition to the darker color signifies P<0.05 in an individual comparison. The dashed orange line indicates the 10% false discovery rate cutoff.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102110&req=5

pone-0020392-g003: Detection of molecular functions experiencing accelerated protein sequence evolution.The dendrogram reflects the proportion of orthologs shared between different categories in our dataset (see Material and Methods). The colors of the corresponding cells and the overlying trace line represent P-values of Mann-Whitney U test for elevated dS, dN, and dN/dS values. The first transition to the darker color signifies P<0.05 in an individual comparison. The dashed orange line indicates the 10% false discovery rate cutoff.
Mentions: We applied Mann-Whitney U (MWU) test to see whether the indices of evolutionary rates were distributed unevenly across functional categories, based on annotations established using Gene Ontology (GO) terms for “biological process” and “molecular function”. Plotting the MWU test P-values across GO categories (Figures 2 and 3, Figures S2 and S3) indicated that the observed dN/dS variation is predominantly driven by variation in dN rates (as expected under varying selection pressures). We visualized a number of functional clusters showing a tendency to rank higher than the rest of the dataset with respect to dN/dS. Several of the highlighted GO categories passed the 10% false discovery rate cutoff [40] (Table 3).

Bottom Line: Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla.The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception.This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.

View Article: PubMed Central - PubMed

Affiliation: Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. christian.voolstra@kaust.edu.sa

ABSTRACT

Background: Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably.

Methodology/principal findings: We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experience adaptive evolution. 7% of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium.

Conclusion/relevance: This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.

Show MeSH
Related in: MedlinePlus