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Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.

Rosic N, Kaniewska P, Chan CK, Ling EY, Edwards D, Dove S, Hoegh-Guldberg O - BMC Genomics (2014)

Bottom Line: Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality.A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels.Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, The University of Queensland, Brisbane Qld 4072, Australia. n.rosic@uq.edu.au.

ABSTRACT

Background: Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality. Understanding how elevated temperatures and nutrient concentration affect early transcriptional changes in corals and their algal endosymbionts is critically important for evaluating the responses of coral reefs to global changes happening in the environment. Here, we investigated the expression of genes in colonies of the reef-building coral Acropora aspera exposed to short-term sub-lethal levels of thermal (+6°C) and nutrient stress (ammonium-enrichment: 20 μM).

Results: The RNA-Seq data provided hundreds of differentially expressed genes (DEGs) corresponding to various stress regimes, with 115 up- and 78 down-regulated genes common to all stress regimes. A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels. Taxonomic analyses of the coral holobiont disclosed the dominant presence of transcripts from coral (~70%) and Symbiodinium (~10-12%), as well as ~15-20% of unknown sequences which lacked sequence identity to known genes. Gene ontology analyses revealed enriched pathways, which led to changes in the dynamics of protein networks affecting growth, cellular processes, and energy requirement.

Conclusions: In corals with preserved symbiont physiological performance (based on Fv/Fm, photo-pigment and symbiont density), transcriptomic changes and DEGs provided important insight into early stages of the stress response in the coral holobiont. Although there were no signs of coral bleaching after exposure to short-term thermal and nutrient stress conditions, we managed to detect oxidative stress and apoptotic changes on a molecular level and provide a list of prospective stress biomarkers for both partners in symbiosis. Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs.

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Related in: MedlinePlus

The DiffKAP pipeline. The schematic diagram of DiffKAP. The pipeline includes the following steps: 1- Produce a k-mer uniqueness plot to predict the optimum k-mer length; 2 - For each dataset, count the total number of each unique k-mer with the optimum length and normalise by dataset size; 3- Identify differentially expressed k-mers (DEKs) by comparing abundance between datasets; 4 - Combine the original read datasets to produce a single set of unique reads; 5 - Identify differentially expressed reads (DERs) based on their composition of DEKs; 6 - The DERs are annotated to present a redundant set of differentially expressed genes (DEGs) and 7 – Finally parse the blastx output file.
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Fig6: The DiffKAP pipeline. The schematic diagram of DiffKAP. The pipeline includes the following steps: 1- Produce a k-mer uniqueness plot to predict the optimum k-mer length; 2 - For each dataset, count the total number of each unique k-mer with the optimum length and normalise by dataset size; 3- Identify differentially expressed k-mers (DEKs) by comparing abundance between datasets; 4 - Combine the original read datasets to produce a single set of unique reads; 5 - Identify differentially expressed reads (DERs) based on their composition of DEKs; 6 - The DERs are annotated to present a redundant set of differentially expressed genes (DEGs) and 7 – Finally parse the blastx output file.

Mentions: The DiffKAP pipeline analyses a pairwise dataset by identifying differentially expressed k-mers (DEKs) first, then obtaining differentially expressed reads (DERs) and finally annotating the DERs to gather differentially expressed genes (DEGs). It consists of seven core processing steps, as shown in Figure 6:Figure 6


Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.

Rosic N, Kaniewska P, Chan CK, Ling EY, Edwards D, Dove S, Hoegh-Guldberg O - BMC Genomics (2014)

The DiffKAP pipeline. The schematic diagram of DiffKAP. The pipeline includes the following steps: 1- Produce a k-mer uniqueness plot to predict the optimum k-mer length; 2 - For each dataset, count the total number of each unique k-mer with the optimum length and normalise by dataset size; 3- Identify differentially expressed k-mers (DEKs) by comparing abundance between datasets; 4 - Combine the original read datasets to produce a single set of unique reads; 5 - Identify differentially expressed reads (DERs) based on their composition of DEKs; 6 - The DERs are annotated to present a redundant set of differentially expressed genes (DEGs) and 7 – Finally parse the blastx output file.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4301396&req=5

Fig6: The DiffKAP pipeline. The schematic diagram of DiffKAP. The pipeline includes the following steps: 1- Produce a k-mer uniqueness plot to predict the optimum k-mer length; 2 - For each dataset, count the total number of each unique k-mer with the optimum length and normalise by dataset size; 3- Identify differentially expressed k-mers (DEKs) by comparing abundance between datasets; 4 - Combine the original read datasets to produce a single set of unique reads; 5 - Identify differentially expressed reads (DERs) based on their composition of DEKs; 6 - The DERs are annotated to present a redundant set of differentially expressed genes (DEGs) and 7 – Finally parse the blastx output file.
Mentions: The DiffKAP pipeline analyses a pairwise dataset by identifying differentially expressed k-mers (DEKs) first, then obtaining differentially expressed reads (DERs) and finally annotating the DERs to gather differentially expressed genes (DEGs). It consists of seven core processing steps, as shown in Figure 6:Figure 6

Bottom Line: Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality.A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels.Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, The University of Queensland, Brisbane Qld 4072, Australia. n.rosic@uq.edu.au.

ABSTRACT

Background: Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality. Understanding how elevated temperatures and nutrient concentration affect early transcriptional changes in corals and their algal endosymbionts is critically important for evaluating the responses of coral reefs to global changes happening in the environment. Here, we investigated the expression of genes in colonies of the reef-building coral Acropora aspera exposed to short-term sub-lethal levels of thermal (+6°C) and nutrient stress (ammonium-enrichment: 20 μM).

Results: The RNA-Seq data provided hundreds of differentially expressed genes (DEGs) corresponding to various stress regimes, with 115 up- and 78 down-regulated genes common to all stress regimes. A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels. Taxonomic analyses of the coral holobiont disclosed the dominant presence of transcripts from coral (~70%) and Symbiodinium (~10-12%), as well as ~15-20% of unknown sequences which lacked sequence identity to known genes. Gene ontology analyses revealed enriched pathways, which led to changes in the dynamics of protein networks affecting growth, cellular processes, and energy requirement.

Conclusions: In corals with preserved symbiont physiological performance (based on Fv/Fm, photo-pigment and symbiont density), transcriptomic changes and DEGs provided important insight into early stages of the stress response in the coral holobiont. Although there were no signs of coral bleaching after exposure to short-term thermal and nutrient stress conditions, we managed to detect oxidative stress and apoptotic changes on a molecular level and provide a list of prospective stress biomarkers for both partners in symbiosis. Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs.

Show MeSH
Related in: MedlinePlus