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Rapid Acclimation Ability Mediated by Transcriptome Changes in Reef-Building Corals.

Bay RA, Palumbi SR - Genome Biol Evol (2015)

Bottom Line: For long-lived organisms, acclimation likely generates a faster response but is only effective if the rates and limits of acclimation match the dynamics of local environmental variation.This is in addition to a previously observed longer term response, distinguishable by its shift in baseline expression, under nonstressful conditions.Such rapid acclimation may provide some protection for this species of coral against slow onset of warming ocean temperatures.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Stanford University rbay@stanford.edu.

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Related in: MedlinePlus

Heat stress response of acclimation-affected gene clusters. The red line shows the probability density of the log2 fold change between stressed and nonstressed samples for a given cluster, identified by comparing gene expression of heat-stressed samples across acclimation treatments. The dotted black line shows the  expectation—the log2 fold change between stressed and nonstressed samples for all contigs—and the gray envelope shows the 95% confidence interval for a randomly sampled group of contigs of the same size as the cluster. The left panel shows cluster 1 (n = 71), which is upregulated during heat stress, whereas the right panel shows cluster 2 (n = 709), which is downregulated during heat stress.
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evv085-F4: Heat stress response of acclimation-affected gene clusters. The red line shows the probability density of the log2 fold change between stressed and nonstressed samples for a given cluster, identified by comparing gene expression of heat-stressed samples across acclimation treatments. The dotted black line shows the expectation—the log2 fold change between stressed and nonstressed samples for all contigs—and the gray envelope shows the 95% confidence interval for a randomly sampled group of contigs of the same size as the cluster. The left panel shows cluster 1 (n = 71), which is upregulated during heat stress, whereas the right panel shows cluster 2 (n = 709), which is downregulated during heat stress.

Mentions: Heat-stressed and nonstressed branches had dramatically different transcriptional profiles. The result is that the total number of reads that could be mapped to the reference transcriptome was larger for the nonstressed samples (P < 0.01; supplementary fig. S3, Supplementary Material online)—transcriptomes generated from nonstressed branches had an average of 3.02 million reads mapped compared with 2.26 million for stressed samples. Of 28,053 contigs, 22,338 (79.6%) yielded significant results (FDR = 0.05) in a negative binomial test for differential expression during heat stress. The difference in total read count is likely the result of a drastic change in expression across many genes, altering total transcription levels. Since normalization methods assume that most genes are not differentially expressed, a gene-by-gene analysis of heat stress expression is not reliable in this case. We can, however, compare the magnitude of change during heat stress across groups of genes. We, therefore, examine the response to acute heat stress of genes in the two clusters we identified as differentially expressed across acclimation treatments. These broad-scale comparisons show us that cluster 1 is upregulated after heat stress (P < 0.01) compared with a random sample, while cluster 2 is downregulated after heat stress (P < 0.01; fig. 4). The stress response seen in the 29 °C acclimated samples is dampened in coral colonies acclimated to higher temperatures (fig. 5; supplementary fig. S4, Supplementary Material online); the magnitude of expression during heat stress is smaller for samples acclimated to either 31 °C or variable (29–33 °C) temperatures. Upon further investigation, we see that this muted response is not the result of a change in baseline expression, but differential expression after heat stress in individuals acclimated to higher temperatures (supplementary fig. S5, Supplementary Material online).Fig. 4.—


Rapid Acclimation Ability Mediated by Transcriptome Changes in Reef-Building Corals.

Bay RA, Palumbi SR - Genome Biol Evol (2015)

Heat stress response of acclimation-affected gene clusters. The red line shows the probability density of the log2 fold change between stressed and nonstressed samples for a given cluster, identified by comparing gene expression of heat-stressed samples across acclimation treatments. The dotted black line shows the  expectation—the log2 fold change between stressed and nonstressed samples for all contigs—and the gray envelope shows the 95% confidence interval for a randomly sampled group of contigs of the same size as the cluster. The left panel shows cluster 1 (n = 71), which is upregulated during heat stress, whereas the right panel shows cluster 2 (n = 709), which is downregulated during heat stress.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494073&req=5

evv085-F4: Heat stress response of acclimation-affected gene clusters. The red line shows the probability density of the log2 fold change between stressed and nonstressed samples for a given cluster, identified by comparing gene expression of heat-stressed samples across acclimation treatments. The dotted black line shows the expectation—the log2 fold change between stressed and nonstressed samples for all contigs—and the gray envelope shows the 95% confidence interval for a randomly sampled group of contigs of the same size as the cluster. The left panel shows cluster 1 (n = 71), which is upregulated during heat stress, whereas the right panel shows cluster 2 (n = 709), which is downregulated during heat stress.
Mentions: Heat-stressed and nonstressed branches had dramatically different transcriptional profiles. The result is that the total number of reads that could be mapped to the reference transcriptome was larger for the nonstressed samples (P < 0.01; supplementary fig. S3, Supplementary Material online)—transcriptomes generated from nonstressed branches had an average of 3.02 million reads mapped compared with 2.26 million for stressed samples. Of 28,053 contigs, 22,338 (79.6%) yielded significant results (FDR = 0.05) in a negative binomial test for differential expression during heat stress. The difference in total read count is likely the result of a drastic change in expression across many genes, altering total transcription levels. Since normalization methods assume that most genes are not differentially expressed, a gene-by-gene analysis of heat stress expression is not reliable in this case. We can, however, compare the magnitude of change during heat stress across groups of genes. We, therefore, examine the response to acute heat stress of genes in the two clusters we identified as differentially expressed across acclimation treatments. These broad-scale comparisons show us that cluster 1 is upregulated after heat stress (P < 0.01) compared with a random sample, while cluster 2 is downregulated after heat stress (P < 0.01; fig. 4). The stress response seen in the 29 °C acclimated samples is dampened in coral colonies acclimated to higher temperatures (fig. 5; supplementary fig. S4, Supplementary Material online); the magnitude of expression during heat stress is smaller for samples acclimated to either 31 °C or variable (29–33 °C) temperatures. Upon further investigation, we see that this muted response is not the result of a change in baseline expression, but differential expression after heat stress in individuals acclimated to higher temperatures (supplementary fig. S5, Supplementary Material online).Fig. 4.—

Bottom Line: For long-lived organisms, acclimation likely generates a faster response but is only effective if the rates and limits of acclimation match the dynamics of local environmental variation.This is in addition to a previously observed longer term response, distinguishable by its shift in baseline expression, under nonstressful conditions.Such rapid acclimation may provide some protection for this species of coral against slow onset of warming ocean temperatures.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Stanford University rbay@stanford.edu.

Show MeSH
Related in: MedlinePlus