Danio rerio and Pomacentrus moluccensis: comparative genomic hybridisation and early gene response to heat stress
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PROVIDER: PRJNA95095 | ENA |
REPOSITORIES: ENA
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Project description:Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we test the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fish species will respond to these increased temperatures and which genes are important for resistance and adaptation to elevated temperatures is not known. Microarray technology may help identify candidate genes for thermal stress resistance in coral reef fishes. Results from a comparative genomic DNA hybridisation experiment and direct sequence comparisons indicate that for most genes there is significant sequence similarity between P. moluccensis and D. rerio, suggesting that the D. rerio array is applicable to P. moluccensis. Heterologous microarray experiments on heat-stressed P. moluccensis identified changes in transcript abundance at 120 gene loci, with many genes involved in protein processing, transcription, and cell growth. Changes in transcript abundance for a selection of candidate genes were confirmed by quantitative real-time PCR. We have demonstrated that heterologous microarrays can be successfully employed to study non-model organisms. Such a strategy thus greatly enhances the applicability of microarray technology to the field of environmental and functional genomics and will be useful for investigating the molecular basis of thermal adaptation in coral reef fishes. Keywords: stress response, comparative genomic hybridization (CGH)
2006-04-30 | GSE4047 | GEO
Project description:Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we test the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fish species will respond to these increased temperatures and which genes are important for resistance and adaptation to elevated temperatures is not known. Microarray technology may help identify candidate genes for thermal stress resistance in coral reef fishes. Results from a comparative genomic DNA hybridisation experiment and direct sequence comparisons indicate that for most genes there is significant sequence similarity between P. moluccensis and D. rerio, suggesting that the D. rerio array is applicable to P. moluccensis. Heterologous microarray experiments on heat-stressed P. moluccensis identified changes in transcript abundance at 120 gene loci, with many genes involved in protein processing, transcription, and cell growth. Changes in transcript abundance for a selection of candidate genes were confirmed by quantitative real-time PCR. We have demonstrated that heterologous microarrays can be successfully employed to study non-model organisms. Such a strategy thus greatly enhances the applicability of microarray technology to the field of environmental and functional genomics and will be useful for investigating the molecular basis of thermal adaptation in coral reef fishes. Keywords: stress response, comparative genomic hybridization (CGH) Common reference design [Stress response_P. moluccensis]: four individual treatment fish (heat-stressed) are contrasted in four microarray hybridisations against a pooled control consisting of four fish kept at ambient temperature. All eight fish employed in this analysis were wild-captured and are biological replicates. The experiment included dye-swap, i.e. stressed fish were labelled red in two hybridisations and green in the other two hybridisations. Common reference design [CGH_P. moluccensis and D. rerio]: four individual P. moluccensis gDNA samples are contrasted in four microarray hybridisations against a pooled gDNA sample consisting of three D. rerio. The experiment included dye-swaps.
2010-06-11 | E-GEOD-4047 | biostudies-arrayexpress
Project description:Environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis
| PRJNA100481 | ENA
Project description:Transcriptional profiling of gene responses in liver in the coral reef fish Pomacentrus moluccensis in response to different types of environmental stress: cold, heat, hypoxic and hyposmotic shock. Goal was to determine the common effects of different types of environmental stress on gene expression as well as responses unique to different stressors. Abstract from Kassahn et al. BMC Genomics (2007) 8:358 Background While our understanding of the importance of transcriptional regulation for biological function is continuously growing, we still know comparatively little about how environmentally-induced stress affects gene expression in vertebrates and how consistent transcriptional stress responses are across different types of environmental stress. Results In this study, we looked for a genetic measure of environmental stress and used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. We identified a series of gene functions that were consistently involved in all stress responses examined here, suggesting common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes and the responses of individual genes varied greatly across different stress types. However, we were able to identify groups of co-regulated genes, the genes within which shared similar functions. Given current estimates of climatic change, we were particularly interested in the response to prolonged heat exposure. In total, 324 gene loci were differentially expressed following exposure to heat over five days. The functions of these heat-responsive genes suggest that prolonged heat stress leads to oxidative stress and protein damage, challenge of the immune system, and a re-allocation of energy sources. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. This study offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future. Keywords: Stress response
2007-10-15 | GSE7499 | GEO