Next-generation transcriptome profiling reveals insights into genetic factors contributing to growth differences and temperature adaptation in Australian populations of barramundi (Lates calcarifer)

Newton, James R.; Zenger, Kyall R.; Jerry, Dean R.

doi:10.1016/j.margen.2013.07.002

Cited by 29 publications

(21 citation statements)

References 31 publications

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“…Some transcripts had multiple annotation hits Porcelli et al 2015 for review). Wide-scale upregulation of HSP70, HSP90 and sHSP families in response to thermal stress is common in a number of fish (Fangue et al 2006;Liu et al 2013;Newton et al 2013;Smith et al 2013), insects (see King & MacRae 2015) and urchins (Runcie et al 2012), including during embryogenesis (Krone et al 1997;Runcie et al 2012). The observed significant increase in expression of hspa8 (aka hsc70) under thermal stress has been suggested to result in higher thermotolerance in fish (Fangue et al 2006) and is similar to observations in the Chinese soft-shelled turtle Pelodiscus sinensis (Li et al 2012).…”

Section: Differential Expression Of Stress-indicator Genessupporting

confidence: 66%

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress

et al. 2017

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Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack of the maternal buffering processes and parental care. Heat-shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat-shock factors (HSFs) have not been determined in reptiles. Here, we subject embryonic sea turtles (Caretta caretta) to a biologically realistic thermal stress and employ de novo transcriptomic profiling of brain tissue to investigate the underlying molecular response. From a reference transcriptome of 302 293 transcripts, 179 were identified as differentially expressed between treatments. As anticipated, genes enriched in the heat-shock treatment were primarily associated with the Hsp families, or were genes whose products play similar protein editing and chaperone functions (e.g. bag3, MYOC and serpinh1). Unexpectedly, genes encoding the HSFs were not significantly upregulated under thermal stress, indicating their presence in unstressed cells in an inactive state. Genes that were downregulated under thermal stress were less well functionally defined but were associated with stress response, development and cellular organization, suggesting that developmental processes may be compromised at realistically high temperatures. These results confirm that genes from the Hsp families play vital roles in the thermal tolerance of developing reptile embryos and, in addition with a number of other genes, should be targets for evaluating the capacity of oviparous reptiles to respond adaptively to the effects of climate change.

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Section: Differential Expression Of Stress-indicator Genessupporting

confidence: 66%

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress

et al. 2017

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“…However, in line with previously observed patterns ( Sørensen et al, 2003 ), hsp70 and hsp90 were also found to be downregulated or constant in longer-duration stress ( Meyer et al , 2011 ; Kenkel et al , 2013 ; Narum et al , 2013 ). In the common garden experiments, genes belonging to Hsp70, Hsp90 and Hsp47 families showed higher constitutive gene expression levels in more thermally tolerant populations ( Schoville et al , 2012 ; Tan et al , 2012 ; Barshis et al , 2013 ; Liu et al , 2013 ; Narum et al 2013 ; Newton et al 2013 ).…”

Section: Literature Reviewmentioning

confidence: 99%

“…In 10 out of 15 studies in which a single population was subjected to a temperature shift and then studied for changes in gene expression, members of both the Hsp70 and Hsp90 gene families were upregulated upon heat stress ( Meyer et al , 2011 ; Runcie et al , 2012 ; Tan et al , 2012 ; Clark et al , 2013 ; Huth and Place, 2013 ; Liu et al , 2013 ; Narum et al , 2013 ; Newton et al , 2013 ; Olsvik et al , 2013 ; Smith et al , 2013 ). However, in line with previously observed patterns ( Sørensen et al, 2003 ), hsp70 and hsp90 were also found to be downregulated or constant in longer-duration stress ( Meyer et al , 2011 ; Kenkel et al , 2013 ; Narum et al , 2013 ).…”

Section: Literature Reviewmentioning

confidence: 99%

The environmental genomics of metazoan thermal adaptation

et al. 2015

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Continued and accelerating change in the thermal environment places an ever-greater priority on understanding how organisms are going to respond. The paradigm of ‘move, adapt or die', regarding ways in which organisms can respond to environmental stressors, stimulates intense efforts to predict the future of biodiversity. Assuming that extinction is an unpalatable outcome, researchers have focussed attention on how organisms can shift in their distribution to stay in the same thermal conditions or can stay in the same place by adapting to a changing thermal environment. How likely these respective outcomes might be depends on the answer to a fundamental evolutionary question, namely what genetic changes underpin adaptation to the thermal environment. The increasing access to and decreasing costs of next-generation sequencing (NGS) technologies, which can be applied to both model and non-model systems, provide a much-needed tool for understanding thermal adaptation. Here we consider broadly what is already known from non-NGS studies about thermal adaptation, then discuss the benefits and challenges of different NGS methodologies to add to this knowledge base. We then review published NGS genomics and transcriptomics studies of thermal adaptation to heat stress in metazoans and compare these results with previous non-NGS patterns. We conclude by summarising emerging patterns of genetic response and discussing future directions using these increasingly common techniques.

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“…At the molecular level, changes in gene expression play an important role in physiological resilience to thermal stress 14 , 28 , 29 . Recent evidence in corals, gobies and barramundi suggested that increased expression of molecular chaperones such as heat shock protein ( Hsp ) genes can repair heat-induced cellular damage 25 , 30 , 31 . More studies have linked transcriptomic responses to organismal thermal tolerance to better explore the mechanisms of thermal adaptation 32 .…”

Section: Introductionmentioning

confidence: 99%

Regional differences in thermal adaptation of a cold-water fish Rhynchocypris oxycephalus revealed by thermal tolerance and transcriptomic responses

Zhang

Shen

et al. 2018

Sci Rep

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Understanding how populations adapt to different thermal environments is an important issue for biodiversity conservation in the context of recent global warming. To test the hypothesis that populations from southern region are more sensitive to climate change than northern region in cold-water species, we determined the thermal tolerance of two geographical populations of a cold-water fish, Rhynchocypris oxycephalus: the Hangzhou population from southern region and the Gaizhou population from northern region, then compared their transcriptomic responses between a control and a high temperature treatment. The results showed that the thermal tolerance range and thermal tolerance polygon area of Hangzhou population were narrower than the Gaizhou population, indicating populations from southern region were possibly more vulnerable. Further transcriptomic analysis revealed that the Gaizhou population expressed more temperature responding genes than the Hangzhou population (583 VS. 484), corresponding with their higher thermal tolerance, while some of these genes (e.g. heat shock protein) showed higher expression in the Hangzhou population under control condition, suggesting individuals from southern region possibly have already responded to the present higher environmental temperature pressure. Therefore, these results confirm the prediction that populations from southern region are more sensitive to global warming, and will be important for their future conservation.

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Next-generation transcriptome profiling reveals insights into genetic factors contributing to growth differences and temperature adaptation in Australian populations of barramundi (Lates calcarifer)

Cited by 29 publications

References 31 publications

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress

The environmental genomics of metazoan thermal adaptation

Regional differences in thermal adaptation of a cold-water fish Rhynchocypris oxycephalus revealed by thermal tolerance and transcriptomic responses

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