Genomics-enabled research in marine ecology: challenges, risks and pay-offs

Hofmann, Gretchen E.; Place, Sean P.

doi:10.3354/meps332249

Cited by 32 publications

(22 citation statements)

References 51 publications

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“…This trend is clearly illustrated within the field of ocean change biology. Whereas only a few years ago discussions regarding the use of transcriptomics in climate-change science were largely hypothetical and focused on how to appropriately implement these tools and expand their application to a broader range of target organisms [42,52,53], genomic resources for marine research have increased to the point where many of these goals have been accomplished. In fact, there presently exists a sufficient mass of geneexpression data related to ocean change to infer trends that could be applied more widely in marine research.…”

Section: Expanding Tool-kits For Conservation Physiologymentioning

confidence: 99%

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

Evans

Hofmann

2012

Phil. Trans. R. Soc. B

147

131

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Anthropogenic stressors, such as climate change, are driving fundamental shifts in the abiotic characteristics of marine ecosystems. As the environmental aspects of our world's oceans deviate from evolved norms, of major concern is whether extant marine species possess the capacity to cope with such rapid change. In what many scientists consider the post-genomic era, tools that exploit the availability of DNA sequence information are being increasingly recognized as relevant to questions surrounding ocean change and marine conservation. In this review, we highlight the application of high-throughput gene-expression profiling, primarily transcriptomics, to the field of marine conservation physiology. Through the use of case studies, we illustrate how gene expression can be used to standardize metrics of sub-lethal stress, track organism condition in natural environments and bypass phylogenetic barriers that hinder the application of other physiological techniques to conservation. When coupled with fine-scale monitoring of environmental variables, gene-expression profiling provides a powerful approach to conservation capable of informing diverse issues related to ocean change, from coral bleaching to the spread of invasive species. Integrating novel approaches capable of improving existing conservation strategies, including gene-expression profiling, will be critical to ensuring the ecological and economic health of the global ocean.

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Section: Expanding Tool-kits For Conservation Physiologymentioning

confidence: 99%

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

Evans

Hofmann

2012

Phil. Trans. R. Soc. B

147

131

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“…This technique is now routinely used in studies of marine ecology (Watanabe & Hamamura 2003, Hofmann & Place 2007, Smith & Osborn 2009, and guidelines have been developed to instruct researchers on how to optimally perform and interpret qPCR experiments (Bustin et al 2009). An essential component of a reliable qPCR assay is the data normalisation: this process controls and corrects for experimental variations that may occur during the extraction, reverse transcription and amplification of RNA (Bustin 2000(Bustin , 2002.…”

Section: Introductionmentioning

confidence: 99%

Strict thermal threshold identified by quantitative PCR in the sponge Rhopaloeides odorabile

Pantile¹,

Webster²

2011

Mar. Ecol. Prog. Ser.

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In light of increasing sea surface temperatures, quantifying the expression of stressinducible genes in coastal organisms is imperative to identify early biomarkers of thermal stress. In the present study we developed a quantitative PCR (qPCR) assay to test the molecular response to heat stress in the Great Barrier Reef sponge Rhopaloeides odorabile. Suitable reference genes (coding for α-tubulin, 28S rRNA and ubiquitin) were identified among 5 candidates and then used to normalise expression of target genes (actin-related protein, calmodulin, ferritin, ubiquitin-conjugating enzyme, heat shock protein 90 [Hsp90] and heat shock protein 40 [Hsp40]) in samples exposed to high temperatures (31 and 32°C) for 1, 3, 14 and 15 d. A rapid down-regulation of most genes (actinrelated protein, ferritin, calmodulin and Hsp90) was observed at both temperatures within 24 h, indicating an initial shut-down of the sponge's molecular systems in response to thermal stress. The increased expression of Hsp40 and Hsp90 in sponges at 32°C after 1 and 3 d respectively indicates an activation of the heat shock response system and is consistent with their role as chaperones for directing degraded proteins to proteolysis, this last process being sustained by an induction of the ubiquitin-conjugating enzyme gene at this temperature. While sponges kept at 32°C only survived for the first 3 d, none of the genes in sponges kept at 31°C were significantly different from those in the 27°C controls after 14 d. This indicates a very strict thermal threshold for R. odorabile between 31 and 32°C and is consistent with previous findings based on sponge necrosis and symbiotic disruptions in this species.KEY WORDS: qPCR · Quantitative PCR · Thermal stress · Porifera · Great Barrier Reef Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 431: [97][98][99][100][101][102][103][104][105] 2011 tance of Porifera, the effect of thermal stress on sponges has rarely been investigated, particularly at the molecular level. The few studies published on this topic include a thermal-stress experiment in which Western blotting was utilised to show that the marine sponge Suberites domuncula ex presses a 45 kDa polypeptide after heat treatment (Bachinski et al. 1997). Moreover, a drop in trehalose (a disaccharide that can protect yeast from temperature stress as shown by Hottiger et al. 1987 andEleutherio et al. 1993), a reduction in the activity of the detoxifying and antioxidant enzyme glutathione-S-transferase (GST) and a concomitant decrease of its substrate glutathione (GSH) were recorded in the same specimens. In heatand cold-stressed Geodia cydonium, an in creased transcription of the heat shock protein 70 (Hsp70) gene and a reduction of the Rab GDP dissociation inhibitor (GDI) mRNA (a key element in the intracellular traffic system) were observed using Northern blotting (Krasko et al. 1997). These findings indicate the presence of active heat-stress protection mechanisms in sponges at the cellular leve...

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“…Recently, genomics-based approaches have allowed a unique view into the mechanisms underlying suites of ecological processes. Notably, transcriptomicsthe measurement of all mRNAs in a biological sampleis quickly emerging in marine ecology, enhancing our understanding of many important ecological and physiological processes in marine systems (for reviews see Hofmann et al 2005, Wilson et al 2005, Dupont et al 2007, Hofmann & Place 2007. The ability to profile the expression patterns of numerous genes at once is expanding investigations into ecological processes ranging from the mechanisms that maintain coral/algal symbioses (Rodriguez-Lanetty et al 2006) to understanding mechanisms underlying physiological tolerances (Podrabsky & Somero 2004, Buckley et al 2006, Teranishi & Stillman 2007 or for detection of disease in commercially important species (Dhar et al 2003, Cunningham et al 2006, Morrison et al 2006.…”

Section: Introductionmentioning

confidence: 99%

Gene expression in the intertidal mussel Mytilus californianus: physiological response to environmental factors on a biogeographic scale

Place¹,

O’Donnell²,

Hofmann

2008

Mar. Ecol. Prog. Ser.

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We used a cDNA microarray to profile gene expression in the intertidal mussel Mytilus californianus across major portions of its biogeographic range. Overall, the expression pattern for the majority of genes assessed in this study varied significantly as a function of collection site and provides support for the hypothesis that the physiological response to emersion is distinct across populations of M. californianus. Gill tissue was dissected from adult, fieldacclimatized M. californianus collected from 4 sites across 17°of latitude along the west coast of North America. First-strand cDNA prepared from 5 biological replicates from each site were competitively hybridized to a 2496 feature cDNA microarray. Gene expression patterns in mussels from Strawberry Hill, Oregon, displayed a unique expression phenotype that was distinct from the other 3 mussel populations sampled. In contrast, mussels sampled from Bamfield, British Columbia, and Jalama Beach, California, showed similar expression patterns. These data suggest that the physiological response of M. californianus to abiotic factors, such as temperature, cannot be predicted by a simple latitudinal gradient. This study highlights the usefulness of genomicsbased approaches in assessing physiological responses to environmental variation across large spatial scales.

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Genomics-enabled research in marine ecology: challenges, risks and pay-offs

Cited by 32 publications

References 51 publications

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

Strict thermal threshold identified by quantitative PCR in the sponge Rhopaloeides odorabile

Gene expression in the intertidal mussel Mytilus californianus: physiological response to environmental factors on a biogeographic scale

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