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Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures.

Mayfield AB, Wang YB, Chen CS, Lin CY, Chen SH - Mol. Ecol. (2014)

Bottom Line: Specimens of the model Indo-Pacific reef coral Pocillopora damicornis collected from upwelling reefs of Southern Taiwan were previously found to have survived a 36-week exposure to 30°C, a temperature they encounter infrequently and one that can elicit the breakdown of the coral-dinoflagellate (genus Symbiodinium) endosymbiosis in many corals of the Pacific Ocean.Specifically, at elevated temperatures, Symbiodinium populations residing within the coral gastrodermal tissues were more likely to up-regulate the expression of genes encoding proteins involved in metabolism than their coral hosts.Collectively, these transcriptome-scale data suggest that the two members of this endosymbiosis have distinct strategies for acclimating to elevated temperatures that are expected to characterize many of Earth's coral reefs in the coming decades.

View Article: PubMed Central - PubMed

Affiliation: National Museum of Marine Biology and Aquarium, 2 Houwan Rd., Checheng, Pingtung, 944, Taiwan; Living Oceans Foundation, 8181 Professional Place, Suite 215, Landover, MD, 20785, USA.

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Functional distribution of differentially expressed genes (DEGs). A gene ontology (GO) was assigned to a high percentage of the 48 288-contig host coral (a) and 15 374-contig Symbiodinium  (b) reference assemblies. A subset of 970 host coral (c) and 879 Symbiodinium (d) DEGs (repeated-measures anova, P < 0.01) was then analysed separately and assigned GO functional category tags. In (c-d), GO categories that were down- or up-regulated relative to the respective reference assembly for each compartment (two-sample proportion test, P < 0.01) are marked with a ‘(−)’ or a ‘(+),’ respectively. When neither icon has been placed next to a GO category in (c–d), the respective GO category was represented at a similar proportion as in the respective reference assembly for that compartment (two-sample proportion test, P > 0.01). GO category percentages that differed significantly between host coral and Symbiodinium DEG pools are denoted by asterisks (‘*’) in (d). In all panels, ‘unknown processes’ refer to contigs for which GO tags could be assigned, although the GOs did not correspond to a particular cellular process (e.g., ‘diabetes’).
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fig02: Functional distribution of differentially expressed genes (DEGs). A gene ontology (GO) was assigned to a high percentage of the 48 288-contig host coral (a) and 15 374-contig Symbiodinium  (b) reference assemblies. A subset of 970 host coral (c) and 879 Symbiodinium (d) DEGs (repeated-measures anova, P < 0.01) was then analysed separately and assigned GO functional category tags. In (c-d), GO categories that were down- or up-regulated relative to the respective reference assembly for each compartment (two-sample proportion test, P < 0.01) are marked with a ‘(−)’ or a ‘(+),’ respectively. When neither icon has been placed next to a GO category in (c–d), the respective GO category was represented at a similar proportion as in the respective reference assembly for that compartment (two-sample proportion test, P > 0.01). GO category percentages that differed significantly between host coral and Symbiodinium DEG pools are denoted by asterisks (‘*’) in (d). In all panels, ‘unknown processes’ refer to contigs for which GO tags could be assigned, although the GOs did not correspond to a particular cellular process (e.g., ‘diabetes’).

Mentions: Genes that were differentially expressed at an α level of 0.01 were used to generate Figs.2 and3a, as well as target DEGs for real-time PCR analysis, described below. To uncover differences in metabolism-targeted gene expression across treatments and compartments (Fig.3b,c), only genes that were differentially expressed at an α level of 0.01 and whose expression levels differed by 2-fold or more between treatments (at either or both sampling times) were included in the analysis. When comparing the total number of DEGs for each compartment (Fig.3a) with a student's t-test, a correction was made to reflect the fact that 3.2-fold more contigs were of host coral origin; the Symbiodinium DEG contig counts were multiplied by 3.2 prior to the statistical tests but are presented as their uncorrected values in the figure itself. Such a correction was unnecessary when calculating the percentage of genes that were differentially expressed (i.e., ‘% DEGs;’ #DEGs/total contig count) in each compartment (sensu Figs.3b and4).


Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures.

Mayfield AB, Wang YB, Chen CS, Lin CY, Chen SH - Mol. Ecol. (2014)

Functional distribution of differentially expressed genes (DEGs). A gene ontology (GO) was assigned to a high percentage of the 48 288-contig host coral (a) and 15 374-contig Symbiodinium  (b) reference assemblies. A subset of 970 host coral (c) and 879 Symbiodinium (d) DEGs (repeated-measures anova, P < 0.01) was then analysed separately and assigned GO functional category tags. In (c-d), GO categories that were down- or up-regulated relative to the respective reference assembly for each compartment (two-sample proportion test, P < 0.01) are marked with a ‘(−)’ or a ‘(+),’ respectively. When neither icon has been placed next to a GO category in (c–d), the respective GO category was represented at a similar proportion as in the respective reference assembly for that compartment (two-sample proportion test, P > 0.01). GO category percentages that differed significantly between host coral and Symbiodinium DEG pools are denoted by asterisks (‘*’) in (d). In all panels, ‘unknown processes’ refer to contigs for which GO tags could be assigned, although the GOs did not correspond to a particular cellular process (e.g., ‘diabetes’).
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig02: Functional distribution of differentially expressed genes (DEGs). A gene ontology (GO) was assigned to a high percentage of the 48 288-contig host coral (a) and 15 374-contig Symbiodinium  (b) reference assemblies. A subset of 970 host coral (c) and 879 Symbiodinium (d) DEGs (repeated-measures anova, P < 0.01) was then analysed separately and assigned GO functional category tags. In (c-d), GO categories that were down- or up-regulated relative to the respective reference assembly for each compartment (two-sample proportion test, P < 0.01) are marked with a ‘(−)’ or a ‘(+),’ respectively. When neither icon has been placed next to a GO category in (c–d), the respective GO category was represented at a similar proportion as in the respective reference assembly for that compartment (two-sample proportion test, P > 0.01). GO category percentages that differed significantly between host coral and Symbiodinium DEG pools are denoted by asterisks (‘*’) in (d). In all panels, ‘unknown processes’ refer to contigs for which GO tags could be assigned, although the GOs did not correspond to a particular cellular process (e.g., ‘diabetes’).
Mentions: Genes that were differentially expressed at an α level of 0.01 were used to generate Figs.2 and3a, as well as target DEGs for real-time PCR analysis, described below. To uncover differences in metabolism-targeted gene expression across treatments and compartments (Fig.3b,c), only genes that were differentially expressed at an α level of 0.01 and whose expression levels differed by 2-fold or more between treatments (at either or both sampling times) were included in the analysis. When comparing the total number of DEGs for each compartment (Fig.3a) with a student's t-test, a correction was made to reflect the fact that 3.2-fold more contigs were of host coral origin; the Symbiodinium DEG contig counts were multiplied by 3.2 prior to the statistical tests but are presented as their uncorrected values in the figure itself. Such a correction was unnecessary when calculating the percentage of genes that were differentially expressed (i.e., ‘% DEGs;’ #DEGs/total contig count) in each compartment (sensu Figs.3b and4).

Bottom Line: Specimens of the model Indo-Pacific reef coral Pocillopora damicornis collected from upwelling reefs of Southern Taiwan were previously found to have survived a 36-week exposure to 30°C, a temperature they encounter infrequently and one that can elicit the breakdown of the coral-dinoflagellate (genus Symbiodinium) endosymbiosis in many corals of the Pacific Ocean.Specifically, at elevated temperatures, Symbiodinium populations residing within the coral gastrodermal tissues were more likely to up-regulate the expression of genes encoding proteins involved in metabolism than their coral hosts.Collectively, these transcriptome-scale data suggest that the two members of this endosymbiosis have distinct strategies for acclimating to elevated temperatures that are expected to characterize many of Earth's coral reefs in the coming decades.

View Article: PubMed Central - PubMed

Affiliation: National Museum of Marine Biology and Aquarium, 2 Houwan Rd., Checheng, Pingtung, 944, Taiwan; Living Oceans Foundation, 8181 Professional Place, Suite 215, Landover, MD, 20785, USA.

Show MeSH
Related in: MedlinePlus