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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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Discrete distribution of dN/dS ratios.The percentages of conserved (black bars) and lineage-specific (grey bars) genes falling into the respective dN/dS classes. Note that dn/ds ratios over 1.8 were pooled for clarity.
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pone-0020392-g001: Discrete distribution of dN/dS ratios.The percentages of conserved (black bars) and lineage-specific (grey bars) genes falling into the respective dN/dS classes. Note that dn/ds ratios over 1.8 were pooled for clarity.

Mentions: Although lineage-specific genes seem to evolve on average significantly faster than annotated genes, there is nonetheless a broad distribution of different rates for both classes (Figure 1). Annotated orthologs were most common at dn/ds<0.5 and successively diminished with increasing dn/ds. In contrast, lineage-specific orthologs were more evenly distributed across dn/ds values between 0 and 0.5, and were in particular present at values >1. We also found potential TRGs with very low divergence rates (dn/ds<0.01), indicative of high conservation. Those genes are particularly interesting as they might have arisen as a result of lineage-specific evolution until they reached an adaptive peak from which further evolution slowed [35]. As a result they are highly conserved between species of the same lineage but cannot be found outside of those lineages. Note that our BLAST-based annotation approach included the cnidarian Nematostella vectensis, so the TRGs are actually restricted even within cnidarians.


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)

Discrete distribution of dN/dS ratios.The percentages of conserved (black bars) and lineage-specific (grey bars) genes falling into the respective dN/dS classes. Note that dn/ds ratios over 1.8 were pooled for clarity.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020392-g001: Discrete distribution of dN/dS ratios.The percentages of conserved (black bars) and lineage-specific (grey bars) genes falling into the respective dN/dS classes. Note that dn/ds ratios over 1.8 were pooled for clarity.
Mentions: Although lineage-specific genes seem to evolve on average significantly faster than annotated genes, there is nonetheless a broad distribution of different rates for both classes (Figure 1). Annotated orthologs were most common at dn/ds<0.5 and successively diminished with increasing dn/ds. In contrast, lineage-specific orthologs were more evenly distributed across dn/ds values between 0 and 0.5, and were in particular present at values >1. We also found potential TRGs with very low divergence rates (dn/ds<0.01), indicative of high conservation. Those genes are particularly interesting as they might have arisen as a result of lineage-specific evolution until they reached an adaptive peak from which further evolution slowed [35]. As a result they are highly conserved between species of the same lineage but cannot be found outside of those lineages. Note that our BLAST-based annotation approach included the cnidarian Nematostella vectensis, so the TRGs are actually restricted even within cnidarians.

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