Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

Abstract

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short-and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

RNA sequencing, de novo assembly and differential analysis of the gill transcriptome of freshwater climbing perch Anabas testudineus after 6 days of seawater exposure

“…The findings from this study extend to the growing body of research on transcriptomic responses of fishes to different environmental stressors, such as exposure to high salinity environments (reviewed by Oomen & Hutchings, ). In particular, the changes in the mRNA expression of genes in the gills of A. testudineus , exposed to 6 days of SW, fall within the functional categories of ion transport, energy production and metabolism and cell volume regulation that were remarkably consistent with those reported in other SW‐acclimated fishes (Brennan et al ., ; Oomen & Hutchings, ), thereby suggesting their relative importance in responding to salinity challenge in various fish species.…”

Molecular biological methods in environmental engineering

“…Herbicides are widely used in food crops, but their RNA sequencing technique was frequently chosen to study transcriptomic responses of non-model organisms, such as fishes, to the environment changes, like salinity, temperature, dissolved oxygen concentration, and pH stress (Oomen and Hutchings, 2017). Comparative transcriptomics are adopted to contrast gene expression variation not within species, but also the variation among species.…”

Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)

“…66 framework of conservation physiology (Connon et al, 2018). As the initial step in gene 68 expression, gene transcription is a key regulator of physiological status and may provide insights 69 into phenotypic plasticity and responses to environmental factors in wild fish (Alvarez et al, 70 2015;Oomen and Hutchings, 2017), constituting an important tool in the conservation 71 physiology toolbox (Madliger et al, 2018). The increased affordability of RNA-sequencing 72 (RNA-seq) technology has facilitated the development of de novo reference transcriptomes for 73 non-model species making it possible to design whole-transcriptomic, or targeted gene-suite (i.e., 74 with tens to hundreds of genes) studies to examine the physiological status of wild fish.…”

“…For instance, variation in the physiological responses of fish 414 can be affected by capture techniques and differences in the environmental conditions 415 experienced prior to capture, as well as factors such as fish sex and age, that may not be able to 416 be easily controlled or accounted for in the field (Simmons et al, 2015). One method to account 417 for this interindividual variation in the physiological responses of wild fish is by increasing the 418 sample size to increase statistical power (Simmons et al, 2015;Oomen and Hutchings, 2017). 419…”