The utility of transcriptomics in fish conservation

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, researchers from the University of California, Davis discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, the researchers examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, they discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.

Schematic representation of a transcriptomic evaluation approach


Transcriptomic approaches such as RNA-Seq involve the sampling of specific tissues (e.g. fish gill) of interest (1), extraction of RNA from the tissue (2), construction of cDNA libraries (3) and use of high-throughput sequencing technology that produce short fragmented reads (4). These fragments are then aligned and assembled based on homology to the reference genome of a closely related species or through a de novo assembly of a reference transcriptome (5). Differential expression of transcripts between samples of interest can then be computed and functionally analyzed towards describing gene interactions and potential consequences (6).

Connon RE, Jeffries KM, Komoroske LM, Todgham AE, Fangue NA. (2018) The utility of transcriptomics in fish conservation. J Exp Biol 221(Pt 2). [article]

Further reading on fish conservation efforts around the globe…

Eyes on the Seas: A Look into the Fisheries Observer Profession Through Stories and Creative Works

These unsung heroes of natural resource management – operating as they do on the fringes of society, often far out on the open sea for months on end – are a little known professional group of people from the public perspective. This is precisely why, several years ago, the “Eyes on the Seas” book project was conceived. A group of like-minded professionals working in the fisheries management field had the visionary idea of bringing the profession more into the public gaze, via a creative initiative intended to showcase the lives of these extraordinary people.

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