Effects of environmental salinity on global and endocrine-specific transcriptomic profiles in the caudal neurosecretory system of salmonid fishes

The caudal neurosecretory system (CNSS) is a fish-specific neuroendocrine complex whose function(s) remain uncertain despite over 60 years of research. Osmoregulatory roles for the CNSS have been hypothesized, but molecular regulation of the CNSS following changes in environmental salinity remains poorly characterized. Therefore, we performed transcriptomics on the CNSS of rainbow trout (Oncorhynchus mykiss) to establish: (1) how the CNSS responds following seawater (SW) transfer, and (2) which endocrine systems contribute to osmoregulatory responses in the CNSS. Responses following SW transfer varied at 24 h versus 168 h, with changes primarily affecting membrane transport and transcriptional processes at 24 h and neuronal processes at 168 h. Components of several osmoregulation-associated endocrine systems were affected (e.g., corticosteroid receptors), including some that have not previously been identified in the CNSS (e.g., calcitonin). Additionally, transcript levels of corticotropin-releasing factor (CRF) peptides-which have osmoregulatory functions and were highly abundant in the CNSS-were approximately twofold higher after 24 h in SW. Therefore, we performed additional experiments investigating CRF peptides in a more euryhaline salmonid, Atlantic salmon (Salmo salar). Smolts had up to 12-fold higher levels of CRF peptide transcripts than parr, but abundance declined following SW transfer. Additionally, CRF transcripts were lower 24 h following freshwater transfer of SW-acclimated salmon. These results suggest that CRF peptides acutely aid in coordinating physiological responses following fluctuations in environmental salinity via anticipatory and/or responsive mechanisms. Collectively, our data indicate that CNSS-mediated production of CRF peptides has osmoregulatory functions and provide a resource for investigations of novel CNSS functions.

Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity.

Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change.

Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential.

An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts.

We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.

Transcriptome Profiling of Long Non-coding RNAs During the Atlantic Salmon Smoltification Process

For salmon aquaculture, one of the most critical phase is the parr-smolt transformation. Studies around this process have mainly focused on physiological changes and the Na⁺/K⁺-ATPase activity during the osmoregulatory activity. However, understanding how the salmon genome regulates the parr-smolt transformation, specifically the molecular mechanisms involved, remains uncovered. This study aimed to explore the transcriptional modulation of long non-coding RNAs (lncRNAs), as key molecular regulators, during the freshwater (FW) to seawater (SW) transfer in Atlantic salmon. Transcriptome sequencing was performed from gill samples of Atlantic salmon adapted from FW to SW through gradual salinity changes from 0 to 30 PSU. The results showed that most transcripts differently modulated were downregulated in all salinity conditions. Relevant biological processes were associated with growth, collagen formation, immune response, metabolism, and heme transport. Notably, 2864 putative lncRNAs were identified in Atlantic salmon gills differently expressed during fish smoltification. The highest number of lncRNAs differently modulated was observed at 30 PSU. Correlation expression analysis suggests putative regulatory roles of lncRNAs with smoltification-related genes. Herein, co-localization of Na⁺/K⁺-ATPase, growth hormone receptor, and thyroid hormone receptor genes with lncRNAs differentially expressed suggest putative regulatory mechanisms in the Atlantic salmon genome. The lncRNAs can be used as novel biomarkers for the fish smoltification process. Here, the lncRNA_145326 and lncRNA_18762 are putatively related to the parr-smolt transfer in Atlantic salmon. This study is the first description of lncRNAs with putative regulatory roles in Atlantic salmon during the SW adaptation.

Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss)

The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection.

Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation

Background

The Arctic charr (Salvelinus alpinus) has a highly seasonal feeding cycle that comprises long periods of voluntary fasting and a short but intense feeding period during summer. Therefore, the charr represents an interesting species for studying appetite-regulating mechanisms in fish.

Results

In this study, we compared the brain transcriptomes of fed and feed deprived charr over a 4 weeks trial during their summer feeding season. Despite prominent differences in body condition between fed and feed deprived charr at the end of the trial, feed deprivation affected the brain transcriptome only slightly. In contrast, the transcriptome differed markedly over time in both fed and feed deprived charr, indicating strong shifts in basic cell metabolic processes possibly due to season, growth, temperature, or combinations thereof. The GO enrichment analysis revealed that many biological processes appeared to change in the same direction in both fed and feed deprived fish. In the feed deprived charr processes linked to oxygen transport and apoptosis were down- and up-regulated, respectively. Known genes encoding for appetite regulators did not respond to feed deprivation. Gene expression of Deiodinase 2 (DIO2), an enzyme implicated in the regulation of seasonal processes in mammals, was lower in response to season and feed deprivation. We further found a higher expression of VGF (non-acronymic) in the feed deprived than in the fed fish. This gene encodes for a neuropeptide associated with the control of energy metabolism in mammals, and has not been studied in relation to regulation of appetite and energy homeostasis in fish.

Conclusions

In the Arctic charr, external and endogenous seasonal factors for example the increase in temperature and their circannual growth cycle, respectively, evoke much stronger responses in the brain than 4 weeks feed deprivation. The absence of a central hunger response in feed deprived charr give support for a strong resilience to the lack of food in this high Arctic species. DIO2 and VGF may play a role in the regulation of energy homeostasis and need to be further studied in seasonal fish.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5874-z) contains supplementary material, which is available to authorized users.

Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study

A continued programme of research is essential to overcome production bottlenecks in any aquacultured fish species. Since the introduction of genetic and molecular techniques, the quality of immune research undertaken in fish has greatly improved. Thousands of species specific cytokine genes have been discovered, which can be used to conduct more sensitive studies to understand how fish physiology is affected by aquaculture environments or disease. Newly available transcriptomic technologies, make it increasingly easier to study the immunogenetics of farmed species for which little data exists. This paper reviews how the application of transcriptomic procedures such as RNA Sequencing (RNA-Seq) can advance fish research. As a case study, we present some preliminary findings using RNA-Seq to identify cytokine related genes in Seriola lalandi. These will allow in-depth investigations to understand the immune responses of these fish in response to environmental change or disease and help in the development of therapeutic approaches.

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

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.

Natural environmental impacts on teleost immune function

The environment in which teleosts exist can experience considerable change. Short-term changes can occur in relation to tidal movements or adverse weather events. Long-term changes can be caused by anthropogenic impacts such as climate change, which can result in changes to temperature, acidity, salinity and oxygen capacity of aquatic environments. These changes can have important impacts on the physiology of an animal, including its immune system. This can have consequences on the well-being of the animal and its ability to protect against pathogens. This review will look at recent investigations of these types of environmental change on the immune response in teleosts.

The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs

Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr Salvelinus alpinus populations in Iceland.  

To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.

The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including lysozyme and natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.

The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.