RNA-seq analyses of Marine Medaka (Oryzias melastigma) reveals salinity responsive transcriptomes in the gills and livers

Integration of microbiomics and metabolomics reveals energy metabolism imbalance in crucian carp (Carassius auratus) under saline-alkaline exposure

The ecological conditions of freshwater aquaculture are deteriorating by degrees in recent years. Consequently, the comprehensive utilization of saline-alkaline water has garnered increasing societal attention. Here, crucian carp (Carassius auratus) were exposed to 20, 40 mmol/L NaHCO3 for 30 days (T, F group). Metabolomic analyses were conducted using UPLC-QTOF/MS, complemented by biochemical and microbiology profiling to elucidate the damage of the saline environment to the intestinal microbial structure, which in turn interfered with the energy metabolism. It was observed that carbonate alkalinity (CA) exposure not only caused intestine oxidative stress but also changed the levels of several digestive enzymes, including α-amylase (AMS), chymotrypsin (CHY), lipase (LPS). Metabolomic analysis identified 22 different metabolites (DEMs) in T group and 77 DEMs in F group. MetaboAnalyst analysis indicated that these metabolites are primarily involved in energy-related pathways, including the citric acid cycle, galactose metabolism, and glycine, serine, and threonine metabolism. Intestinal microbial diversity and community composition were altered under carbonate alkalinity exposure, with increase in Proteobacteria abundance and decline in Firmicutes, abundance alongside enrichment of Sphingomonas. Herein, saline-alkaline stress disrupted the physiological homeostasis of the crucian carp intestine, leading to microbial dysbiosis and energy metabolic imbalance. This study provides a theoretical foundation for understanding the stress response of the crucian carp intestine and the role of the intestinal microbiome in host resilience under adverse environmental conditions.

Genome-Wide Analysis Reveals Expansion and Positive Selection of Monocarboxylate Transporter Genes Linked to Enhanced Salinity and Ammonia Tolerance in Sinonovacula constricta

Our previous genome analysis of Sinonovacula constricta revealed an expansion of the monocarboxylate transporter gene family, which is crucial for metabolic dynamic balance and intracellular pH regulation. To further elucidate the role of these expanded MCT genes in response to variable environmental conditions, we conducted a comprehensive genome-wide identification, phylogenetic evolution and expression analysis. In this study, 16 sodium-coupled monocarboxylate transporter genes (designated as ScSMCTs) and 54 proton-coupled monocarboxylate transporter genes (designated as ScMCTs) were identified from the S. constricta genome. The results of gene number comparison indicated significant expansion of ScSMCTs and ScMCTs in mollusks compared to vertebrates, likely due to tandem repeats and dispersed duplications in S. constricta. The syntenic analysis demonstrated that the razor-clam MCT genes had the highest number of homologous gene pairs with Meretrix meretrix. The phylogenetic tree showed that MCT and SMCT proteins were distinctly clustered in two large branches. Moreover, positive selection analysis revealed three positive selection sites in the MCT amino acid sequences sites. Multi-transcriptome analyses and the temporal expression patterns displayed that ScSMCTs and ScMCTs play distinct roles in response to salinity and ammonia stressors. It is worth noting that the majority of these genes involved in abiotic stresses belong to MCTs. Overall, our findings revealed the important roles of ScSMCTs and ScMCTs under abiotic stress, and provided valuable information for the evolution of this family in mollusks, as well as a theoretical basis for the further study of the mechanism and function of this gene family in S. constricta.

Effects of short-term salt exposure on gill damage, serum components and gene expression patterns in juvenile Largemouth bass (Micropterus salmoides)

The Largemouth bass (Micropterus salmoides; LMB) is a freshwater fish that plays a significant role in aquaculture, and its cultural base is expanding into inland saline water areas. To study the effect of short-term salt exposure on LMB, fish with an average body weight of 11.69 (±1.82) g were cultured for 14 days at three different salt concentrations (0 ‰, 6 ‰, and 12 ‰). After 14 days, the second gill arch was collected for tissue sectioning and transcriptome sequencing, while serum samples were collected to analyze serum components. The results showed that the mortality rate in the 0 ‰ and 6 ‰ groups was 0 %, whereas the mortality rate in the 12 ‰ group was 62 %. In the gill tissue sections, no apparent damage was observed in the 0 ‰ and 6 ‰ groups. However, in the 12 ‰ group, the secondary lamellae became shorter, thicker, and exhibited a disordered arrangement. The serum component test results showed that osmolality and K+ significantly increased in the 12 ‰ group, while Na+, K+, and Cl- concentrations showed slight increases, but the differences were not significant. Comparative transcriptome analysis revealed that, along the salinity gradient, gene expression exhibited five profiles. Genes related to ion transport and immunity were highly expressed in the 6 ‰ and 12 ‰ groups, while genes associated with biosynthesis and ATP production showed decreased expression levels as salinity increased. Notably, seven solute carrier genes, two Na+/K+-ATPase genes, and two insulin-like growth factor genes were significantly highly expressed in the 12 ‰ salinity group, playing important roles in the transmembrane transport of ions. Based on the results, the LMB can acclimatize to a salt concentration of at least 6 ‰. However, exposure to 12 ‰ salinity can lead to a series of adverse effects, including organ damage, reduced energy metabolism efficiency, and disruption of ion homeostasis.

Kidney transcriptome analysis reveals the molecular responses to salinity adaptation in largemouth bass (Micropterus salmoides)

Recently, against the background of increasing land salinization and global warming, many studies have examined the mechanisms of freshwater fish adaptation to elevated salinity. However, the mechanisms underlying salinity tolerance in the kidney of Micropterus salmoides, a popular saline aquaculture species, remain poorly understood. We used RNA-seq to explore the differentially expressed genes (DEGs) in the kidney of M. salmoides at 0 ‰, 5 ‰, and 10 ‰ salinity for 24 d and 48 d. These DEGs mainly affected metabolism-related pathways, such as secondary metabolite biosynthesis, arachidonic acid metabolism, etc., and immunity-related pathways, such as IL-17 signaling and ECM-receptor interaction. Trend analysis on days 24 and 48 showed that, as salinity increased, the up-regulated genes were notably enriched in the cytochrome P450 xenobiotic metabolic pathway, and down-regulated genes substantially linked to cell cycle, phagosome, etc. More importantly, we identified a total of 22 genes enriched in the cytochrome P450 xenobiotic metabolic pathway, including seven UDP-glucuronosyltransferase genes (UGTs) and five glutathione S-transferase genes (GSTs). We speculated that M. salmoides kidneys removed toxic substances produced due to salinity stress and mitigated oxidative damage by up-regulating UGTs and GSTs, hence maintaining normal physiological function. In addition, genes such as Cystatin A1, significantly up-regulated with increasing salinity stress and duration, favoured the recovery of kidney injury. This research delved into the molecular processes involved in the adaptability of M. salmoides to high salinity stress and provided valuable information for the future breeding of salinity-tolerant strains.

Transcriptomics and proteomics provide insights into the adaptative strategies of Tibetan naked carps (Gymnocypris przewalskii) to saline-alkaline variations

Gymnocypris przewalskii is an exclusively cyprinid fish that inhabits Lake Qinghai, which is characterized by high salinity and alkalinity. To elucidate the molecular basis of the adaptation of G. przewalskii to a wide range of salinity‒alkalinity conditions, we performed morphological, biochemical, transcriptomic and proteomic analyses of the major osmoregulatory organs of the gills and kidney. Morphological examination revealed that mitochondria-rich cells were replaced by mucus cells in the gills during the transition of G. przewalskii from freshwater to lake water. In the kidney, the tight junction formed dense structure in the renal tubules under lake water condition compared with the loose structure in freshwater. The results of the biochemical assays revealed an increased content of total amino acids, indicating their potential roles as osmolytes and energy supplies in freshwater. The decreased urea concentration suggested that urea synthesis might not be involved in the detoxicity of ammonia. The transcriptomic and proteomic data revealed that genes involved in ion absorption and ammonia excretion were activated in freshwater and that genes involved in cell junction and glutamine synthesis were induced in lake water, which was consistent with the morphological and biochemical observations. Together with the higher levels of glutamine and glutamate, we proposed that G. przewalskii alleviated the toxic effect of ammonia direct excretion through gills under freshwater and the activation of the conversion of glutamate to glutamine under high saline-alkaline condition. Our results revealed different expression profiles of genes involved in metabolic pathways, including the upregulation of genes involved in energy production in freshwater and the induction of genes involved in the synthesis of acetylneuramic acid and sphingolipid in soda lake water. In conclusion, the appearance of mitochondria-rich cells and increased energy production might contribute to ion absorption in G. przewalskii to maintain ion and solute homeostasis in freshwater. The existence of mucus cells and dense junctions, which are associated with increased gene expression, might be related to the adaptation of G. przewalskii to high salinity-alkalinity.

How short-term change in temperature or salinity affect cellular immune parameters of three-spined stickleback, Gasterosteus aculeatus?

Reference values for the non-specific immune response of stickleback have been developed to better understand the natural variability of the immunomarkers and to increase their relevance for the detection of environmental perturbations. However, under field conditions, temperature and salinity can vary from station to station and their influence on the reference ranges of the immunomarkers should therefore be quantified. To this end, adult sticklebacks were exposed either to different temperatures (from 12 to 18 °C) or to different salinities (from 0 to 30 g/L) for 21 days after 10 days of acclimatization. The results were then projected onto reference ranges to better determine the effect of temperature and salinity on the innate immune response. With the exception of leucocyte necrosis at higher temperature and respiratory burst at lower temperature, previously established reference ranges for immunomarkers of sticklebacks were suitable when variations in temperature and salinity were tested. Finally, this study argues for the possibility of using stickleback and its immune reference range in the field regardless of temperature and salinity, due to its relatively temperature and salinity independent innate immune response. Reference ranges for immunomarkers in stickleback could be a real added value to water quality diagnosis in biomonitoring programs in variable seasonal and geographical environmental contexts. Furthermore, these results confirm the rapid adaptability of sticklebacks to different variations in temperature and salinity without affecting their immunological parameters.

TPT disrupts early embryonic development and glucose metabolism of marine medaka in different salinites

Triphenyltin (TPT) is an organotin compound frequently detected in coastal estuaries, yet studies on TPT's effects in regions with significant salinity fluctuations, such as coastal estuaries, are currently limited. To investigate the toxic effects of TPT under different salinity conditions, this study focused on marine medaka (Oryzias melastigma) embryos. Through early morphological observations, RNA-seq analysis, biochemical marker assays, and qPCR detection, we explored the impact of TPT exposure on the early embryonic development of marine medaka under varying salinities. The study found that TPT exposure significantly increased embryo mortality at salinities of 0 ppt and 30 ppt. RNA-seq analysis revealed that TPT primarily affects glucose metabolism and glycogen synthesis processes in embryos. Under high salinity conditions, TPT may inhibit glucose metabolism by suppressing glycolysis and promoting gluconeogenesis. Furthermore, TPT exposure under different salinities led to the downregulation of genes associated with the insulin signaling pathway (ins, insra, irs2b, pik3ca, pdk1b, akt1, foxo1a), which may be linked to suppressed glucose metabolism and increased embryonic mortality. In summary, TPT exposure under different salinities affects the early development of marine medaka embryos and inhibits glucose metabolism. This study provides additional data to support research on organotin compounds in coastal estuaries.

Exploitation of Key Regulatory Modules and Genes for High-Salt Adaptation in Schizothoracine by Weighted Gene Co-Expression Network Analysis

Schizothoracine fishes in saltwater lakes of the Tibetan Plateau are important models for studying the evolution and uplift of the Tibetan Plateau. Examining their adaptation to the high-salt environment is interesting. In this study, we first assembled the RNA-Seq data of each tissue of G. przewalskii, G. selincuoensis, and G. namensis from Qinghai Lake, Selincuo Lake, and Namtso Lake, respectively, obtained by the group previously. After obtaining reliable results, the adaptation of the gills, kidneys, and livers of the three species to the high-salinity environment was assessed by weighted gene co-expression network analysis (WGCNA). Using module eigengenes (ME), 21, 22, and 22 gene modules were identified for G. przewalskii, G. selincuoensis, and G. nemesis, respectively. Functional clustering analysis of genes in the significant association module identified several genes associated with osmolarity-regulated potential KEGG pathways in the gills of three species of Schizothoracine fish. Th17 cell differentiation pathway was up-regulated in the gills of all three species; histocompatibility class 2 II antigen and E alpha (h2-ea) were up-regulated genes in this pathway. Functional clustering analysis of genes in apparently related modules in the kidney unveiled several differential KEGG pathways. The pentose phosphate pathway was up-regulated in the three Schizothoracine fishes, and glucose-6-phosphate dehydrogenase (g6pd) was an up-regulated gene in this pathway. In the livers of the three Schizothorax species, the propanoate metabolism pathway was up-regulated, and succinate-CoA ligase GDP-forming subunit beta (suclg2) was an up-regulated gene in this pathway. The above analyses provide reference data for the adaptation of Schizothorax to high-salt environments and lay the foundation for future studies on the adaptive mechanism of Schizothorax in the plateau. These results partly fill the void in the knowledge gap in the survival adaptations of Schizothoracine fishes to highland saline lakes.

Genome-wide identification of 769 G protein-coupled receptor (GPCR) genes from the marine medaka Oryzias melastigma

The marine medaka Oryzias melastigma is a useful fish model for marine and estuarine ecotoxicology studies and can be applied to field-based population genomics because of its distribution in Asian estuaries and other coastal areas. We identified 769 full-length G protein-coupled receptor genes in the O. melastigma genome and classified them into five distinct classes. A phylogenetic comparison of GPCR genes in O. melastigma to humans and two other small fish species revealed a high-level orthological relationship. Purinergic and chemokine receptors were highly differentiated in humans whereas significant differentiation of chemosensory receptors was evident in fish species. Our results suggest that the GPCR gene families among the species used in this study exhibit evidence of sporadic evolutionary processes. These results may help improve our understanding of the advanced repertoires of GPCR and expand our knowledge of physiological mechanisms of fish in response to various environmental stimuli.

Structure and gene expression changes of the gill and liver in juvenile black porgy (Acanthopagrus schlegelii) under different salinities

Black porgy (Acanthopagrus schlegelii) is an important marine aquaculture species in China. It is an ideal object for the cultivation of low-salinity aquaculture strains in marine fish and the study of salinity tolerance mechanisms in fish because of its strong low-salinity tolerance ability. Gill is the main osmoregulatory organ in fish, and the liver plays an important role in the adaptation of the organism to stressful environments. In order to understand the coping mechanisms of the gills and livers of black porgy in different salinity environments, this study explored these organs after 30 days of culture in hypoosmotic (0.5 ppt), isosmotic (12 ppt), and normal seawater (28 ppt) at histologic, physiologic, and transcriptomic levels. The findings indicated that gill exhibited a higher number of differentially expressed genes than the liver, emphasizing the gill's heightened sensitivity to salinity changes. Protein interaction networks and enrichment analyses highlighted energy metabolism as a key regulatory focus at both 0.5 ppt and 12 ppt salinity in gills. Additionally, gills showed enrichment in ions, substance transport, and other metabolic pathways, suggesting a more direct regulatory response to salinity stress. The liver's regulatory patterns at different salinities exhibited significant distinctions, with pathways and genes related to metabolism, immunity, and antioxidants predominantly activated at 0.5 ppt, and molecular processes linked to cell proliferation taking precedence at 12 ppt salinity. Furthermore, the study revealed a reduction in the volume of the interlamellar cell mass (ILCM) of the gills, enhancing the contact area of the gill lamellae with water. At 0.5 ppt salinity, hepatic antioxidant enzyme activity increased, accompanied by oxidative stress damage. Conversely, at 12 ppt salinity, gill NKA activity significantly decreased without notable changes in liver structure. These results underscore the profound impact of salinity on gill structure and function, highlighting the crucial role of the liver in adapting to salinity environments.

Effect of salinity on the physiological response and transcriptome of spotted seabass (Lateolabrax maculatus)

Salinity fluctuations significantly impact the reproduction, growth, development, as well as physiological and metabolic activities of fish. To explore the osmoregulation mechanism of aquatic organisms acclimating to salinity stress, the physiological and transcriptomic characteristics of spotted seabass (Lateolabrax maculatus) in response to varying salinity gradients were investigated. In this study, different salinity stress exerted inhibitory effects on lipase activity, while the impact on amylase activity was not statistically significant. Notably, a moderate increase in salinity (24 psu) demonstrated the potential to enhance the efficient utilization of proteins by spotted seabass. Both Na+/K+-ATPase and malondialdehyde showed a fluctuating trend of increasing and then decreasing, peaking at 72 h. Transcriptomic analysis revealed that most differentially expressed genes were involved in energy metabolism, signal transduction, the immune response, and osmoregulation. These results will provide insights into the molecular mechanisms of salinity adaptation and contribute to sustainable development of the global aquaculture industry.

Population genomics analysis to identify ion and water transporter genes involved in the adaptation of Tibetan naked carps to brackish water

Understanding how evolutionary processes shape the genetic variations and influence the response of species to environmental alterations is critical for biodiversity conservation and molecular breeding. Gymnocypris przewalskii przewalskii is the only known cyprinid fish that dwells in the brackish water of Lake Qinghai on the Qinghai-Tibetan Plateau. To reveal the genetic basis of its adaptation to high salinity and alkalinity, whole-genome sequencing was performed in G. p. przewalskii and its freshwater relatives Gymnocypris eckloni and Gymnocypris przewalskii ganzihonensis. Compared with freshwater species, lower genetic diversity and higher linkage disequilibrium were observed in G. p. przewalskii. Selective sweep analysis identified 424 core-selective genes enriched in transport activities. Transfection analysis showed that genetic changes in the positively selected gene aquaporin 3 (AQP3) improved cell viability after salt treatment, suggesting its involvement in brackish water adaptation. Our analysis indicates that ion and water transporter genes experienced intensive selection, which might have contributed to the maintenance of high osmolality and ion content in G. p. przewalskii. The current study identified key molecules involved in the adaptation of fish to brackish water, providing valuable genomic resources for the molecular breeding of salt-tolerant fish.

The role of the microbiome on fish mucosal immunity under changing environments

The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.

Systematic toxicological analysis of the effect of salinity on the physiological stress induced by triphenyltin in Nile tilapia

Triphenyltin (TPT), a synthetic chemical, is prevalent in complex salinity areas, including estuaries and coastal regions. However, current studies on the toxicological effects of TPT relevant to the environment at different salinities are limited. In the study, biochemical, histological, and transcriptional analyses of TPT and salinity alone, or in combination, was performed on the Nile tilapia (Oreochromis niloticus) liver. Nile tilapia exhibited weakened antioxidant defenses and liver damage. Transcriptomic analysis revealed that TPT exposure primarily affected lipid metabolism and immunity; salinity exposure alone particularly affected carbohydrate metabolism; combined exposure primarily immune- and metabolic-related signaling pathways. In addition, the single exposure to TPT or salinity induced inflammatory responses by up-regulating the expression of pro-inflammatory cytokines, whereas combined exposure suppressed inflammation by down-regulating pro-inflammatory cytokine levels. These findings are beneficial to understand the negative effects of TPT exposure in Nile tilapia in the broad salinity zones and its potential defense mechanisms.

The role of salinity in recovery of white sturgeon (Acipenser transmontanus) from stimulated angling stress

White sturgeon (Acipenser transmontanus) in the Lower Fraser River are the focus of a catch-and-release angling fishery in British Columbia, Canada. However, the lower region of the catch area includes areas where tidal waters invade, and the consequence of salinity levels on recovery from an angling challenge are not characterized in sturgeon, despite theoretical implications of its import. We acclimated white sturgeon to various salinities (0, 10 and 20‰ (parts per thousand)) to investigate the effects of acclimation on recovery from stimulated angling stress that was induced through manual chasing. This challenge elicited the traditional physiological responses such as ion homeostasis disturbance, increases in secondary stress indicators and metabolic acidosis; however, environmental salinity altered the timing of recovery in some of the parameters measured. In addition, the severity of the intracellular pH disturbance in both heart and red blood cell seemed to be mediated in fresh water, yet the recovery pattern of plasma chloride and bicarbonate ions seemed to be facilitated by higher salinity. In general, responses were similar but not identical, leading us to conclude that the role of salinity on recovery from exercise is complex but not insignificant. Salinity may be important to behaviours exhibited by white sturgeon (such as migrations) in their respective saline environments, but less so around the impact of an angling stressor. Further exploration of this response may provide insight on whether the current tidal boundaries for angling white sturgeon are appropriate.

Transcriptome analysis and gene expression analysis related to salinity-alkalinity and low temperature adaptation of Triplophysa yarkandensis

T. yarkandensis is a common species of Triplophysa, and it is distributed in Shule river of Hexi Corridor, of Gansu province in China. In order to enrich gene database resources and explore the environment adaptation of T. yarkandensis, fifteen tissues were collected from three adult T. yarkandensis for transcriptome sequencing and de novo assembly. Nine major international gene annotation databases (NR, COG, egg_NOG, TrEMBL, Pfam, KOG, Swiss prot, KEGG and Gene Ontology) were utilized to annotate unigenes. A detailed study was conducted to explore the gene expression and the differentially expressed genes among five tissues (brain, heart, kidney, liver and spleen). In addition, the current study showed that candidate genes involved in salinity-alkalinity and low temperature adaptation were differentially expressed in tissues of T. yarkandensis. Precisely, mapk1, abcc1, gpx1, gpx4, cat and aqp1 genes participated in the regulation process of salinity-alkalinity adaptation, and elovl4, acaca, fasn, acaa2, acox1 and acox3 genes were involved in fatty acid metabolism and closely associated with low temperature adaptation. On the one hand, it was found that the expression of these genes varied among different tissues, and the important pathways involved in these genes were mapped. Furthermore, we analyzed mapk1 and acox1 genes in depth to obtain the predicted gene structure and important amino acid sites. The transcriptome information in this study will be conducive to provide further understanding for the molecular level research and exploration of the environmental adaptation of T. yarkandensis.

Transcriptomic Analysis in Marine Medaka Gill Reveals That the Hypo-Osmotic Stress Could Alter the Immune Response via the IL17 Signaling Pathway

Fish gills are the major osmoregulatory tissue that contact the external water environment and have developed an effective osmoregulatory mechanism to maintain cellular function. Marine medaka (Oryzias melastigma) has the ability to live in both seawater and fresh water environments. The present study performed a seawater (SW) to 50% seawater (SFW) transfer, and the gill samples were used for comparative transcriptomic analysis to study the alteration of hypo-osmotic stress on immune responsive genes in this model organism. The result identified 518 differentiated expressed genes (DEGs) after the SW to SFW transfer. Various pathways such as p53 signaling, forkhead box O signaling, and the cell cycle were enriched. Moreover, the immune system was highlighted as one of the top altered biological processes in the enrichment analysis. Various cytokines, chemokines, and inflammatory genes that participate in the IL-17 signaling pathway were suppressed after the SW to SFW transfer. On the other hand, some immunoglobulin-related genes were up-regulated. The results were further validated by real-time qPCR. Taken together, our study provides additional gill transcriptome information in marine medaka; it also supports the notion that osmotic stress could influence the immune responses in fish gills.

Genome-wide identification and expression analysis of mitogen-activated protein kinase (MAPK) genes in response to salinity stress in channel catfish (Ictalurus punctatus)

The mitogen-activated protein kinase (MAPK) gene family has been systematically described in several fish species, but less so in channel catfish (Ictalurus punctatus), which is an important global aquaculture species. In this study, 16 MAPK genes were identified in the channel catfish genome and classified into three subfamilies based on phylogenetic analysis, including six extracellular signal regulated kinase (ERK) genes, six p38-MAPK genes and four C-Jun N-terminal kinase (JNK) genes. All MAPK genes were distributed unevenly across 10 chromosomes, of which three (IpMAPK8, IpMAPK12 and IpMAPK14) underwent teleost-specific whole genome duplication during evolution. Gene expression profiles in channel catfish during salinity stress were analysed using transcriptome sequencing and qRT-PCR (quantitative reverse transcription PCR). Results from reads per kilobase million (RPKM) analysis showed IpMAPK13, IpMAPK14a and IpMAPK14b genes were differentially expressed when compared with other genes between treatment and control groups. Furthermore, three of these genes were validated by qRT-PCR, of which IpMAPK14a expression levels were significantly upregulated in treatment groups (high and low salinity) when compared with the control group, with the highest expression levels in the low salinity group (P < 0.05). Therefore, IpMAPK14a may have important response roles to salinity stress in channel catfish.

Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis

Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na⁺/K⁺-ATPase and Ca²⁺/Mg²⁺-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na⁺/K⁺ATPase and Ca²⁺/Mg²⁺-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.

Physiological, morphological and transcriptomic responses of Tibetan naked carps (Gymnocypris przewalskii) to salinity variations

Gymnocypris przewalskii is a native cyprinid fish that dwells in the Lake Qinghai with salinity of 12-13‰. It migrates annually to the freshwater rivers for spawning, experiencing the significant changes in salinity. In the present study, we performed the physiological, morphological and transcriptomic analyses to understand the osmoregulation in G. przewalskii. The physiological assay showed that the osmotic pressure of G. przewalskii was almost isosmotic to the brackish lake water. The low salinity reduced its ionic concentrations and osmotic pressure. The plasticity of gill microstructure was linked to the salinity variations, including the presence of mucus and intact tight junctions in brackish water and the development of the mitochondria-rich cells and the loosened tight junctions in freshwater. RNA-seq analysis identified 1926 differentially expressed genes, including 710 and 1216 down- and up-regulated genes in freshwater, which were enriched in ion transport, cell-cell adhesion, and mucus secretion. Genes in ion uptake were activated in low salinity, and mucus pathways and tight junction showed the higher transcription in brackish water. The isosmoticity between the body fluid and the environment suggested G. przewalskii was in the metabolic-saving condition in the brackish water. The decreased salinity disrupted this balance, which activated the ion uptake in freshwater to maintain osmotic homeostasis. The gill remodeling was involved in this process through the development of the mitochondria-rich cells to enhance ion uptake. The current finding provided insights into the potential mechanisms of G. przewalskii to cope with salinity alteration.

Transcriptional Contribution of Transposable Elements in Relation to Salinity Conditions in Teleosts and Silencing Mechanisms Involved

Fish are an interesting taxon comprising species adapted to a wide range of environments. In this work, we analyzed the transcriptional contribution of transposable elements (TEs) in the gill transcriptomes of three fish species exposed to different salinity conditions. We considered the giant marbled eel Anguilla marmorata and the chum salmon Oncorhynchus keta, both diadromous, and the marine medaka Oryzias melastigma, an euryhaline organism sensu stricto. Our analyses revealed an interesting activity of TEs in the case of juvenile eels, commonly adapted to salty water, when exposed to brackish and freshwater conditions. Moreover, the expression assessment of genes involved in TE silencing mechanisms (six in heterochromatin formation, fourteen known to be part of the nucleosome remodeling deacetylase (NuRD) complex, and four of the Argonaute subfamily) unveiled that they are active. Finally, our results evidenced for the first time a krüppel-associated box (KRAB)-like domain specific to actinopterygians that, together with TRIM33, might allow the functioning of NuRD complex also in fish species. The possible interaction between these two proteins was supported by structural prediction analyses.