Transcriptional responses of olive flounder (Paralichthys olivaceus) to low temperature

Cloning of down-regulated genes under cold stress and identification of important genes related to cold tolerance in zebrafish (Danio rerio)

Low-temperature stress poses a significant risk to the survival of both cultivated and wild fish populations. Existing studies have found that the pre-acclimation of fishes to moderate cold stress can stimulate the activation of acclimation pathways, thereby enhancing their tolerance to cold stress. The fitness of fish relies heavily on appropriately controlled transcriptional reactions to environmental changes. Despite previous characterization of gene expression profiles in various fish species during cold acclimation, the specific genes responsible for essential functions in this process remain largely unknown, particularly the down-regulated genes induced by cold acclimation. To investigate the genes involved in cold acclimation, this study employed real-time quantitative PCR (RT-qPCR), molecular cloning, microinjection techniques, and cold stress experiments to determine the genes that play an essential part in cold acclimation. Consequently, 18 genes were discovered to be down-regulated in larval zebrafish experiencing cold stress. All 18 genes successfully detected overexpression in zebrafish at 96 and 126 hpf (fold change ≥3), which declined with the growth of zebrafish. Following microinjection, it was observed that her8a, cyp51, lss, txnipb, and bhlha9 had an adverse impact on the survival rate of zebrafish larvae under cold stress. These genes have been identified to play significant roles in various biological processes. For instance, bhlha9 has been found to be involved in both limb development and temperature sensing and her8a has been implicated in neural development. Additionally, cyp51 and lss have been identified as participants in the cholesterol synthesis pathway. Txnipb has been reported to induce cell apoptosis, thereby potentially influencing the survival rate of zebrafish larvae under cold stress. These findings offered crucial data for the analysis of molecular processes related to cold tolerance and the development of cold-resistant fish breeding.

Systematic assessment of the antifungal mechanism of soil fumigant methyl isothiocyanate against Fusarium oxysporum

Fusarium oxysporum is an important phytopathogenic fungus, it can be controlled by the soil fumigant methyl isothiocyanate (MITC). However, the antimicrobial mechanism of MITC against F. oxysporum, especially at the transcriptional level, is still unclear. In this experiment, the antimicrobial mechanism of MITC against F. oxysporum was investigated. Our results indicated that when F. oxysporum was exposed to 6 mg/L MITC for 12 h, the inhibitory rate of MITC on F. oxysporum was 80%. Transmission electron microscopes showed that the cell wall and membrane of F. oxysporum had shrunk and folded, vacuoles increased, and mitochondria swelled and deformed. In addition, the enzyme activity of F. oxysporum treated with MITC showed a decrease of 32.50%, 8.28% and 74.04% in catalase, peroxidase and superoxide dismutase, respectively. Transcriptome sequencing of F. oxysporum was performed and the results showed that 1478 differentially expressed genes (DEGs) were produced in response to MITC exposure. GO and KEGG analysis showed that the DEGs identified were involved in substance and energy metabolism, signal transduction, transport and catalysis. MITC disrupted cell homeostasis by influencing the expression of some key genes involved in chitin synthase and detoxification enzymes production, but F. oxysporum also protected itself by up-regulating genes involved in energy synthesis (such as upregulating acnA, CS and LSC2 in TCA). qRT-PCR data validated the reliability of transcriptome data. Our research used biochemical and genetic techniques to identify molecular lesions in the mycelia of F. oxysporum exposed to MITC, and provide valuable insights into the toxic mechanism of pathogenic fungi mediated by MITC. These techniques are also likely to be useful for rapidly screening and identifying new, environmentally-friendly soil fumigants that are efficacious against fungal pathogens.

Acute cold stress leads to zebrafish ovarian dysfunction by regulating miRNA and mRNA

Temperature is a critical factor that regulates the reproduction processes in teleost. However, the gonadal response mechanism to cold stress in fish remains largely unknown. In the present study, female zebrafish were exposed to different extents of low temperatures at 18 °C and 10 °C for 48 h. The ovarian histology was remarkably damaged after cold stress exposure. Integrated analysis of miRNA-mRNA was used to investigate the ovarian response to acute cold stress. A large number of mRNAs and miRNAs were altered by cold stress, which are involved in extensive biological processes. It is indicated that the signal transduction of MAPK and Calcium signaling pathway is highly engaged in zebrafish ovary to adapt to cold stress. The immune system was dysregulated by cold stress while the ovarian autophagy was activated. Remarkably increased gene number related to reproductive functions was identified in the cold stress at 10 °C compared to the control. The cold stress-induced dysregulated reproductive genes include star, hsd3b1, hsd17b1, inha, insl3, amh, nanos1 and foxl2. Combined with the dysregulated insulin, IGF and progesterone signaling, it is suggested that cold stress affects ovarian function in multiple aspects, including oocyte meiosis, folliculogenesis, final maturation and ovarian maintenance. On the other hand, the ovarian miRNA-mRNA regulatory network response to cold stress was also constructed. Overall, our result revealed the ovarian response to cold stress in zebrafish and provided insight into the fish adaptation mechanism to acute temperature change.

Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure

Teleost fish have evolved various adaptations that allow them to tolerate cold water conditions. However, the underlying mechanism of this adaptation is poorly understood in Tibetan Plateau fish. RNA-seq combined with liquid chromatography‒mass spectrometry (LC‒MS/MS) metabolomics was used to investigate the physiological responses of a Tibetan Plateau-specific teleost, Gymnocypris przewalskii, under cold conditions. The 8-month G. przewalskii juvenile fish were exposed to cold (4 ℃, cold acclimation, CA) and warm (17 ℃, normal temperature, NT) temperature water for 15 days. Then, the transcript profiles of eight tissues, including the brain, gill, heart, intestine, hepatopancreas, kidney, muscle, and skin, were evaluated by transcriptome sequencing. The metabolites of the intestine, hepatopancreas, and muscle were identified by LC‒MS/MS. A total of 5,745 differentially expressed genes (DEGs) were obtained in the CA group. The key DEGs were annotated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The DEGs from the eight tissues were significantly enriched in spliceosome pathways, indicating that activated alternative splicing is a critical biological process that occurs in the tissues to help fish cope with cold stress. Additionally, 82, 97, and 66 differentially expressed metabolites were identified in the intestine, hepatopancreas, and muscle, respectively. Glutathione metabolism was the only overlapping significant pathway between the transcriptome and metabolome analyses in these three tissues, indicating that an activated antioxidative process was triggered during cold stress. In combination with the multitissue transcriptome and metabolome, we established a physiology-gene‒metabolite interaction network related to energy metabolism during cold stress and found that gluconeogenesis and long-chain fatty acid metabolism played critical roles in glucose homeostasis and energy supply.

Untargeted LC-MS metabolomics reveals the metabolic responses in olive flounder subjected to hirame rhabdovirus infection

Hirame novirhabdovirus (HIRRV), which mainly infects the olive flounder (Paralichthys olivaceus), is considered to be one of the most serious viral pathogens threatening the global fish culture industry. However, little is known about the mechanism of host-pathogen interactions at the metabolomic level. In this study, in order to explore the metabolic response of olive flounder to HIRRV infection, liquid chromatography mass spectrometry (LC-MS) was used to detect the changes of endogenous compounds of the olive flounder after HIRRV infection. A total of 954 unique masses were obtained, including 495 metabolites and 459 lipids. Among them, 7 and 173 qualified differential metabolites were identified at 2 days and 7 days post-infection, respectively. Distinct metabolic profiles were observed along with viral infection. At the early stage of infection, only a few metabolites were perturbed. Among them, the level of inosine and carnosine were increased and the potential antiviral ability of these two metabolites was further confirmed by exogenous addition experiment. At the late stage of HIRRV infection, the metabolic profiles changed remarkably. The changes in amino acids and nucleotides especially the 7-methylguanine also accelerated the amplification of viral particles. And the down-regulation of glutathione (GSH) implied an elevated level of ROS (reactive oxygen species) that attenuated the immune system of flounders. HIRRV also induced the accumulation of purine and reduction of pyrimidine, and elevated LPC and LPE levels. The unbalanced purine/pyrimidine and altered lipid profile may be beneficial for the replication and infection of HIRRV at the late stage of infection. These findings provide new insights into the pathogenic mechanism of HIRRV infection in olive flounder.

Transcriptomics Reveal the Effects of Breeding Temperature on Growth and Metabolism in the Early Developmental Stage of Platax teira

The growth, development, and survival of fish, especially in the early stages of development, is influenced by a complex of environmental factors, among which temperature is one of the most important. Although the physiological effects of environmental stress in fish have been extensively studied, the molecular mechanisms are poorly understood. However, recent advances in transcriptomic techniques have facilitated the study of the molecular mechanisms of environmental stress responses in aquatic species. Here, we aimed to elucidate the effects of breeding temperatures (21, 24, 27, and 30 °C) on the growth and nutrient metabolism in the early developmental stage of Platax teira, using transcriptomic techniques. Transcriptomic analysis identified 5492, 6937, and 4246 differentially expressed genes (DEGs) in the 21 vs. 24 °C, 27 vs. 24 °C, and 30 vs. 24 °C comparisons, respectively, most of which were involved in cell processes, single organism, metabolism, catalytic activity, and cell part, based on gene ontology (GO) functional annotations. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were mainly enriched in pathways related to metabolism of matter and energy, protein digestion and absorption, and glucose and lipid metabolism. Additionally, the expression of genes related to energy, lipid, and glucose metabolism in the fish liver was upregulated under a low-temperature condition (21 °C), although increasing the temperature within the acceptable threshold improved nutrient metabolism and growth in the fish. Meanwhile, nutrient metabolism and growth were suppressed by an extremely high temperature (30 °C) owing to oxidative stress. Overall, it was shown that nutrient metabolism pathways were involved in thermal stress responses in P. teira, and the optimal breeding temperature range was 24-27 °C. Through transcriptomics, the regulatory mechanism of larval development in P. teira under different growth temperatures was elucidated, with the goal of establishing a theoretical basis for industrial breeding.

Replacement Effect of Fish Meal by Plant Protein Sources in Olive Flounder (Paralichthys olivaceus) Feeds with an Addition of Jack Mackerel Meal on Growth, Feed Availability, and Biochemical Composition

Application of feed stimulants is very helpful to increase the feed intake of fish, especially in the development of low fish meal (FM) diets. FM replacement effect by various plant protein sources (corn gluten meal (CGM), soy protein concentrate (SPC), and corn protein concentrate (CPC)) in diets with an addition of jack mackerel meal (JMM) as feed stimulants on growth, feed availability, and biochemical composition of olive flounder was elucidated. An experimental design of two-way (two replacement levels (25% and 50%) × 3 replacement sources (CGM, SPC, and CPC)) analysis of variance was adopted. Seven diets were formulated. Amount of 60% FM was contained in the control (Con) diet. In the Con diet, 25% and 50% FM were replaced by CGM, SPC, and CPC with an addition of 12% JMM as feed stimulants, referred to as the CGM25, CGM50, SPC25, SPC50, CPC25, and CPC50 diets, respectively. Four hundred and twenty juvenile fish were distributed into 21 flow-through tanks. All diets were assigned to triplicate groups of fish. Fish were hand-fed to satiation twice a day for 56 days. Both dietary replacement levels and sources had statistical effect on weight gain (P < 0.0001 and P < 0.045, respectively), specific growth rate (SGR) (P < 0.0001 and P < 0.033), and feed consumption (P < 0.0001 and P < 0.03) of fish. Dietary increased FM replacement levels lowered weight gain, SGR, and feed consumption of fish. Weight gain, SGR, and feed consumption of fish fed the Con and CGM25 diets were statistically (P < 0.05) greater than those of fish fed the CGM50, SPC50, and CPC50 diets. Both replacement level and source had no statistical effect on feed utilization, biochemical composition except for statistical effect of replacement source on glycine content of fish, and lysozyme and superoxide dismutase (SOD) activities of fish. FM up to 25% could be substituted with CGM, SPC, and CPC in the olive flounder feeds supplemented with 12% JMM as feed stimulants without compromising growth, feed utilization, and lysozyme and SOD activities.

LC-MS/MS based characterisation and differential expression of proteins in Himalayan snow trout, Schizothorax labiatus using LFQ technique

Molecular characterization of fish muscle proteins are nowadays considered as a key component to understand the role of specific proteins involved in various physiological and metabolic processes including their up and down regulation in the organisms. Coldwater fish specimens including snow trouts hold different types of proteins which help them to survive in highly diversified temperatures fluctuating from 0 to 20 °C. So, in current study, the liquid chromatography mass spectrometry using label free quantification technique has been used to investigate the muscle proteome profile of Schizothorax labiatus. For proteomic study, two weight groups of S. labiatus were taken from river Sindh. The proteomic analysis of group 1 revealed that a total of 235 proteins in male and 238 in female fish were recorded. However, when male and female S. labiatus were compared with each other on the basis of spectral count and abundance of peptides by ProteinLynx Global Server software, a total of 14 down-regulated and 22 up-regulated proteins were noted in this group. The highly down-regulated ones included homeodomain protein HoxA2b, retinol-binding protein 4, MHC class II beta chain and proopiomelanocortin while as the highly expressed up-regulated proteins comprised of gonadotropin I beta subunit, NADH dehydrogenase subunit 4, manganese superoxide dismutase, recombinase-activating protein 2, glycosyltransferase, chymotrypsin and cytochrome b. On the other hand, the proteomic characterisation of group 2 of S. labiatus revealed that a total of 227 proteins in male and 194 in female fish were recorded. When male and female S. labiatus were compared with each other by label free quantification, a total of 20 down-regulated and 18 up-regulated proteins were recorded. The down-regulated protein expression of group 2 comprised hepatic lipase, allograft inflammatory factor-1, NADH dehydrogenase subunit 4 and myostatin 1 while the highly expressed up-regulated proteins included glycogen synthase kinase-3 beta variant 2, glycogen synthase kinase-3 beta variant 5, cholecystokinin, glycogen synthase kinase-3 beta variant 3 and cytochrome b. Significant (P < 0.05) difference in the expression of down-regulated and up-regulated proteins was also noted between the two sexes of S. labiatus in each group. According to MS analysis, the proteins primarily concerned with the growth, skeletal muscle development and metabolism were down-regulated in river Sindh, which indicates that growth of fish during the season of collection i.e., winter was slow owing to less food availability, gonad development and low metabolic activity. While, the proteins related to immune response of fish were also noted to be down-regulated thereby signifying that the ecosystem has less pollution loads, microbial, pathogenic and anthropogenic activities. It was also found that the proteins involved in glycogen metabolism, reproductive and metabolic processes, particularly lipid metabolism were up-regulated in S. labiatus. The significant expression of these proteins may be connected to pre-spawning, gonad development and use of stored food as source of energy. The information generated in this study can be applied to future research aimed at enhancing food traceability, food safety, risk management and authenticity analysis.

Transcriptomic Networks Reveal the Tissue-Specific Cold Shock Responses in Japanese Flounder (Paralichthys olivaceus)

Low temperature is among the important factors affecting the distribution, survival, growth, and physiology of aquatic animals. In this study, coordinated transcriptomic responses to 10 °C acute cold stress were investigated in the gills, hearts, livers, and spleens of Japanese flounder (Paralichthys olivaceus), an important aquaculture species in east Asia. Histological examination suggested different levels of injury among P. olivaceus tissues after cold shock, mainly in the gills and livers. Based on transcriptome and weighted gene coexpression network analysis, 10 tissue-specific cold responsive modules (CRMs) were identified, revealing a cascade of cellular responses to cold stress. Specifically, five upregulated CRMs were enriched with induced differentially expressed genes (DEGs), mainly corresponding to the functions of "extracellular matrix", "cytoskeleton", and "oxidoreductase activity", indicating the induced cellular response to cold shock. The "cell cycle/division" and "DNA complex" functions were enriched in the downregulated CRMs for all four tissues, which comprised inhibited DEGs, suggesting that even with tissue-specific responses, cold shock may induce severely disrupted cellular functions in all tissues, reducing aquaculture productivity. Therefore, our results revealed the tissue-specific regulation of the cellular response to low-temperature stress, which warrants further investigation and provides more comprehensive insights for the conservation and cultivation of P. olivaceus in cold water.

Temperature induces metabolic reprogramming in fish during bacterial infection

Water temperature elevation as a consequence of global warming results in increased incidence of bacterial disease, such as edwardsiellosis, in fish farming. Edwardsiellosis is caused by the bacterial pathogen Edwardsiella tarda and affects many farmed fish including flounder (Paralichthys olivaceus). Currently, the effect of temperature on the metabolic response of flounder to E. tarda infection is unclear. In this study, we found that compared to low temperature (15°C), high temperature (23°C) enhanced E. tarda dissemination in flounder tissues. To examine the impact of temperature on the metabolism of flounder induced by E. tarda, comparative metabolomics were performed, which identified a large number of metabolites responsive to E. tarda invasion and temperature alteration. During E. tarda infection, the metabolic profile induced by elevated temperature was mainly featured by extensively decreased amino acids and TCA intermediates such as succinate, a proven immune regulator. Further, 38 potential metabolite markers of temperature effect (MMTE) in association with bacterial infection were identified. When used as exogenous supplements, two of the MMTE, i.e., L-methionine and UDP-glucose, effectively upregulated the expression of pro-inflammatory cytokines and suppressed E. tarda infection in flounder leukocytes. Taken together, the results of this study indicate an important influence of temperature on the metabolism of flounder during bacterial infection, which eventually affects the survivability of the fish.

Energy consumption and intestinal microbiome disorders of yellow catfish (Pelteobagrus fulvidraco) under cold stress

The yellow catfish (P. fulvidraco), as one of the economically-relevant freshwater fish found in China, cannot tolerate cold stress. Understanding the physiological and biochemical mechanisms under cold stress may provide insights for improving yellow catfish management in the cold. Therefore, we investigated the metabolic and intestinal microbiota changes in cold stress in response to induced cold stress. We found that cold stress in yellow catfish lead to a significant increase in the consumption of glucose and triglycerides, as well as increased use of cholesterol as an alternate energy source. Moreover, cold stress also activated several significant biological processes in the fish such as thermogenesis, oxidative phosphorylation, the spliceosome machinery, RNA transport, protein processing that occurs in the ER, and purine and pyrimidine metabolism pathways involved in energy production. On the other hand, many other mechanisms like insulin resistance, starch and sucrose metabolism, and the glyoxylate and dicarboxylate metabolic pathways that also served as energy production pathways were weakened. Furthermore, organic acids and their derivatives as well as the lipids and lipid-like molecules were mainly altered in cold stress; prenol lipids, steroids, and their derivatives were significantly upregulated, while fatty acyls and glycerophospholipids were significantly downregulated. Transcriptomic and metabolomic integrated analysis data revealed that carbohydrate metabolism, lipid metabolism, amino acid metabolism, and nucleotide metabolism were involved in cold stress resistance. In addition, the intestinal microbiota abundance was also reduce and the pathogenic bacteria of plesiomonas was rapidly appreciation, which suggesting that cold stress also impaired intestinal health. This research study could offer insights into winter management or the development of feed to promote cold resistance in yellow catfish.

An updated review of cold shock and cold stress in fish

Temperature is critical in regulating virtually all biological functions in fish. Low temperature stress (cold shock/stress) is an often-overlooked challenge that many fish face as a result of both natural events and anthropogenic activities. In this study, we present an updated review of the cold shock literature based on a comprehensive literature search, following an initial review on the subject by M.R. Donaldson and colleagues, published in a 2008 volume of this journal. We focus on how knowledge on cold shock and fish has evolved over the past decade, describing advances in the understanding of the generalized stress response in fish under cold stress, what metrics may be used to quantify cold stress and what knowledge gaps remain to be addressed in future research. We also describe the relevance of cold shock as it pertains to environmental managers, policymakers and industry professionals, including practical applications of cold shock. Although substantial progress has been made in addressing some of the knowledge gaps identified a decade ago, other topics (e.g., population-level effects and interactions between primary, secondary and tertiary stress responses) have received little or no attention despite their significance to fish biology and thermal stress. Approaches using combinations of primary, secondary and tertiary stress responses are crucial as a research priority to better understand the mechanisms underlying cold shock responses, from short-term physiological changes to individual- and population-level effects, thereby providing researchers with better means of quantifying cold shock in laboratory and field settings.

Molecular Mechanism Based on Histopathology, Antioxidant System and Transcriptomic Profiles in Heat Stress Response in the Gills of Japanese Flounder

As an economically important flatfish in Asia, Japanese flounder is threatened by continuously rising temperatures due to global warming. To understand the molecular responses of this species to temperature stress, adult Japanese flounder individuals were treated with two kinds of heat stress—a gradual temperature rise (GTR) and an abrupt temperature rise (ATR)—in aquaria under experimental conditions. Changes in histopathology, programmed cell death levels and the oxidative stress status of gills were investigated. Histopathology showed that the damage caused by ATR stress was more serious. TUNEL signals confirmed this result, showing more programmed cell death in the ATR group. In addition, reactive oxygen species (ROS) levels and the 8-O-hDG contents of both the GTR and ATR groups increased significantly, and the total superoxide dismutase (T-SOD) activities and total antioxidant capacity (T-AOC) levels decreased in the two stressed groups, which showed damage to antioxidant systems. Meanwhile, RNA-seq was utilized to illustrate the molecular mechanisms underyling gill damage. Compared to the control group of 18 °C, 507 differentially expressed genes (DEGs) were screened in the GTR group; 341 were up-regulated and 166 were down-regulated, and pathway enrichment analysis indicated that they were involved in regulation and adaptation, including chaperone and folding catalyst pathways, the mitogen-activated protein kinase signaling (MAPK) pathway and DNA replication protein pathways. After ATR stress, 1070 DEGs were identified, 627 were up-regulated and 423 were down-regulated, and most DEGs were involved in chaperone and folding catalyst and DNA-related pathways, such as DNA replication proteins and nucleotide excision repair. The annotation of DEGs showed the great importance of heat shock proteins (HSPs) in protecting Japanese flounder from heat stress injury; 12 hsp genes were found after GTR, while 5 hsp genes were found after ATR. In summary, our study records gill dysfunction after heat stress, with different response patterns observed in the two experimental designs; chaperones were activated to defend heat stress after GTR, while replication was almost abandoned due to the severe damage consequent on ATR stress.

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.

Transcriptome profiling of olive flounder responses under acute and chronic heat stress

BACKGROUND

The olive flounder (Paralichthys olivaceus) is a saltwater fish, which is valuable to the economy. The olive flounder strives to adapt to environmental stressors through physiological, biochemical, and transcriptional responses. The rise in water temperature threatens the growth, development, reproduction, and survival of olive flounder. Each organ in the olive flounder can differentially respond to heat stress.

OBJECTIVES

The purpose of this study is to investigate organ-specific transcriptional changes in olive flounder tissues during heat stress.

METHODS

In this study, transcriptome dynamics of the gill, liver, and muscle of olive flounder to acute or chronic heat stress were investigated.

RESULTS

Principal component analysis plotting revealed that the transcriptome of each organ is quite separated. K-means clustering, gene ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the differential transcriptome responses of each organ to heat stress. Heat stress commonly affects the pathways involved in the correct protein folding, DNA repair, and cell cycle.

CONCLUSION

Our results may provide a valuable molecular basis of heat acclimation in fishes.

Gene expression changes in response to low temperatures in embryos of the kelp grouper, Epinephelus moara

The kelp grouper Epinephelus moara has high economic value and is popular in fisheries and aquaculture in China. In the previous study, we treated the embryos at 16-22 somite stage at 4 °C, -25.7 °C, -140 °C and -196 °C, and successfully obtained surviving embryos in each group. To better understand the molecular changes affected by the low temperatures, we conducted a comparative transcriptome analysis among embryos exposed at 4 °C for 30 min, embryos exposed at -25.7 °C for 30 min and the control group. qPCR assays were conducted for the validation. Signal transduction pathways were highly enriched for the differentially expressed genes. c-Fos, c-Jun, JunD, GADD45, involved in MAPK signaling pathway, were upregulated when embryos were treated at low temperatures. As immediate early genes, Egr-1a and b, and IER2, that respond quickly to the environment stress, their expression increased as well. Hsp70 showed similar expression pattern as immediate early genes. Meanwhile, transcription factors Sox, HES, TFIID, muscle movement and protein synthesis-related genes were downregulated. Taken together, our findings suggest that cooling disrupts gene expression patterns in E. moara embryos. The differentially expressed genes may be involved in cellular resistance against low temperatures, possibly through neural activation, apoptosis, proliferation, differentiation, cellular recovery and heat shock regulation. This study also provides transcriptome dataset of E. moara embryos exposed to cold temperatures for future studies focusing on the molecular effects of cryopreservation.

Miocene Diversification and High-Altitude Adaptation of Parnassius Butterflies (Lepidoptera: Papilionidae) in Qinghai-Tibet Plateau Revealed by Large-Scale Transcriptomic Data

Simple Summary

Parnassius butterflies have contributed to fundamental studies in biogeography, insect–plant interactions, and other fields of conservation biology and ecology. However, the early evolutionary pattern and molecular adaptation mechanism of this alpine butterfly group to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now. In this study, we report for the first time, a relatively large-scale transcriptomic dataset of eight Parnassius species and their two closely related papilionid species, a dated phylogeny based on hundreds of gene sequences, and potential genetic mechanisms underlying the high-altitude adaptation by investigating changes in evolutionary rates and positively selected genes. Overall, our findings indicate that the transcriptome data sets reported here can provide some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, and will support further expressional and functional studies that will help interested researchers to address evolution, biodiversity and conservation questions concerning Parnassius and other butterfly species.

Abstract

The early evolutionary pattern and molecular adaptation mechanism of alpine Parnassius butterflies to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now, due to difficulties in sampling, limited sequence data, and time calibration issues. Here, we present large-scale transcriptomic datasets of eight representative Parnassius species to reveal the phylogenetic timescale and potential genetic basis for high-altitude adaptation with multiple analytic strategies using 476 orthologous genes. Our phylogenetic results strongly supported that the subgenus Parnassius formed a well-resolved basal clade, and the subgenera Tadumia and Kailasius were closely related in the phylogenetic trees. In addition, molecular dating analyses showed that the Parnassius began to diverge at about 13.0 to 14.3 million years ago (middle Miocene), correlated with their hostplant’s spatiotemporal distributions, as well as geological and palaeoenvironmental changes of the Qinghai–Tibet Plateau. Moreover, the accelerated evolutionary rate, candidate positively selected genes and their potentially functional changes were detected, probably contributed to the high-altitude adaptation of Parnassius species. Overall, our study provided some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, which will help to address evolution, biodiversity, and conservation questions concerning Parnassius and other butterfly species.

Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.)

Properly regulated transcriptional responses to environmental perturbations are critical for the fitness of fish. Although gene expression profiles in the tissues of common carp upon cold stress were previously characterized, the transcriptional programs underlying cold acclimation are still not well known. In this study, the ability of three common carp strains including Hebao red carp (HB), Songpu mirror carp (SPM) and Yellow river carp (YR) to establish cold resistance after acclimation to a mild hypothermia stress at 18°C for 24 h was confirmed by measurements of the critical thermal minimums (CTMin). The gene expression profiles of the brain and the heart from these strains under both control and cold-acclimated conditions were characterized with RNA-sequencing. The data of the three common carp strains with different genetic background were combined in the differential gene expression analyses to balance the effects of genetic diversity on gene expression. Marked effects of tissue origins on the cold-induced transcriptional responses were revealed by comparing the differentially expressed gene (DEG) lists of the two tissues. Functional categories including spliceosome and RNA splicing were highly enriched in the DEGs of both tissues. However, steroid biosynthesis was specifically enriched in DEGs of the brain and response to unfolded protein was solely enriched in DEGs of the heart. Consistent with the up-regulation of the genes involved in cholesterol biosynthesis, total cholesterol content of the brain was significantly increased upon cold stress. Moreover, cold-induced alternative splicing (AS) events were explored and AS of the rbmx (RNA-binding motif protein, X chromosome) gene was confirmed by real-time quantitative PCR. Finally, a core set of cold responsive genes (CRGs) were defined by comparative transcriptomic analyses. Our data provide insights into the transcriptional programs underlying cold acclimation of common carp and offer valuable clues for further investigating the genetic determinants for cold resistance of farmed fish.

Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

Background

Closely related species of the carp family (Cyprinidae) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknown. In this study, we compared transcriptomic profiles of two carp species to identify key factors and pathways for cold tolerance and acclimation.

Results

Larvae of Songpu mirror carp and Barbless carp that were pretreated at 18 °C for 24 h significantly improved their survival rates under lethal cold temperature at 8 °C or 10 °C, indicating that two carp species possess the ability of cold acclimation. However, Songpu mirror carp exhibited stronger abilities of cold tolerance and acclimation than Barbless carp. Transcriptomic profiles of Songpu mirror carp and Barbless carp larvae at 28 °C and 18 °C were compared during cold acclimation through RNA-seq. Differentially expressed genes that are closely associated with the differences in cold acclimation between two carp species were identified through bioinformatics and Venn’s diagram analysis. GO enrichment analysis of these genes indicated that cellular component assembly involved in morphogenesis, secondary alcohol metabolism and drug transport were the most up-regulated biological processes during cold acclimation of Songpu mirror carp. Conversely, positive regulation of macroautophagy, intracellular protein transport, and organonitrogen compound catabolism were the most down-regulated biological processes during cold acclimation of Barbless carp. KEGG enrichment analysis revealed that factors in the FoxO-related signaling pathways are mainly responsible for the development of differences in cold tolerance and acclimation between two carp species since altering the phosphorylation of key proteins in the FoxO-related signaling pathways with inhibitors or an activator significantly decreased the cold tolerance and acclimation of Songpu mirror carp. These data provided key clues for dissection of molecular mechanisms underlying the development of cold tolerance and acclimation in carps.

Conclusions

These findings indicate that larvae of two carp species possess different abilities of cold tolerance and can build cold acclimation under mild low temperature. Multiple biological processes and FoxO-related signaling pathways are closely associated with the development of differences in cold tolerance and acclimation between two carp species.

Insight into AMPK regulation mechanism in vivo and in vitro: Responses to low temperatures in the olive flounder Paralichthys olivaceus

The olive flounder, Paralichthys olivaceus, is a commercially important maricultured fish in China, Japan, and Korea. Low winter temperatures influence its survival and growth and affect the output of the aquaculture industry. Energy metabolism is essential for fish survival, and the central energy-regulating factor - 5'-AMP-activated protein kinase (AMPK) - plays an important role in responses to cold stress. However, the mechanism of AMPK pathway regulation in fish coping with cold stress remains poorly understood. In the present study, the expression of AMPK and its upstream (LKB1 and CaMKKβ) and downstream genes (SITR1, FOXO1A, and TFAM) in the brain, muscle, and heart was analyzed while the flounder was under cold stress (0.2 ± 0.2 °C). The results showed that low temperatures activated LKB1, CaMKKβ, and AMPK genes in the brain, and the activated AMPK induced expression of SITR1, FOXO1A, and TFAM. In the muscle tissue, the expression patterns of these genes presented a trend of initially decreasing and then increasing, and there was a delay in the response to low temperatures. At the cellular level, comparative analysis of the effects of the activator 5-aminoimidazole-4-carboxamide1-β-D-ribofuranoside (AICAR) and inhibitor compound C of the AMPK pathway demonstrated that cold stress was similar to AICAR, which activated the AMPK pathway with hysteresis. Thus, the regulation mechanism of AMPK under cold stress was preliminarily analyzed. In general, AMPK was involved not only in responses to low temperatures but also in energy regulation under cold stress.

Feed and Disease at Olive Flounder (Paralichthys olivaceus) Farms in Korea

The objective of this study was to conduct field experiments comparing formulated (extruded pellets (E.P)) and raw-fish (moist pellets (M.P)) feeds at two flounder aquaculture farms for six months to obtain the basic data necessary for improving aquafarmers’ awareness of feed-quality issues and firmly establish and expand the use of formulated feed. According to the results, the M.P group was higher in weight gain, feed efficiency ratio, protein efficiency ratio, and specific growth rate and lower in mortality rate than the E.P group. All cases of mortality were caused by six kinds of disease, four of which (Vibrio sp., Edwardsiella sp., Streptococcus sp., and Scuticociliates) were common to the two groups, whereas Lymphocystis arose only in the M.P group and abdominal inflation only in the E.P group at both farms. As for mortality in the present experiment, the numbers were 1047 at Da-Hae farm and 1167 at Global farm, with more fish dying in the E.P tanks than in the M.P tanks. By multiplying the number of deaths by selling price, the economic losses were $9650 and $10,756, respectively. Therefore, it should be considered an urgent priority to develop flounder-exclusive formulated feed for improved digestion and absorption rate and also to establish a water-quality-improvement management plan.

Transcriptome sequencing analysis reveals silver nanoparticles antifungal molecular mechanism of the soil fungi Fusarium solani species complex

Silver nanoparticles (AgNPs) have been widely used in various fields due to their antimicrobial activities. However, the antimicrobial mechanisms of AgNPs against fungi, especially on transcriptional level, are still unclear. In this study, the inhibitory property of AgNPs against Fusarium solani species complex was investigated. Transmission electron microscopes were used to observe the alterations in morphology and cellular structure of fungal hyphae treated with AgNPs. Disturbances in the cell walls and membranes, as well as empty space in the cytoplasm were observed. The transcriptome sequencing of F. solani species complex mycelia was performed using the Illumina NextSeq 500 ribonucleic acid sequencing (RNA-Seq) platform. In the RNA-Seq study, AgNPs treatment resulted in 2503 differentially expressed genes (DEGs). Gene Ontology (GO) analysis revealed that the DEGs were mainly involved in 6 different terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis also revealed that energy and substance metabolism, signal transduction and genetic information processing were the most highly enriched pathways for these DEGs. In addition, RNA-seq results were validated by quantitative polymerase chain reactions (qPCRs). Our findings enhanced the understanding of the antifungal activities of AgNPs and the underlying molecular mechanisms, and provided a new perspective for investigating this novel antifungal agent.

Transcriptome analyses provide the first insight into the molecular basis of cold tolerance in Larimichthys polyactis

Larimichthys polyactis is one of the most economically important marine fish species that have become newly cultured in China in recent years. The gene expression changes that L. polyactis experiences in cold toleranceis still unknown, limiting the expansion of its cultivation, fast growth, and high yield. To investigate the molecular mechanism behind L. polyactis's cold tolerance and to provide a resource for conducting genetic research on L. polyactis, transcriptome sequencing using RNA-seq was performed on individuals that survived cold stress at 4 °C (cold tolerant, CT), and individuals that barely survived 4 °C (cold sensitive, CS), which was considered as the control. A number of 387,607,550 clean reads were obtained from the transcriptomes, and comparative transcriptomic analysis identified 141 differently expressed genes (DEGs), of which 67 were up-regulated and 74 were down-regulated in CT compared to CS under cold stress. Furthermore, ten differently expressed genes were selected from the RNA-Seq analysis to be further validated by real-time PCR. Functional network analysis indicated that L. polyactis adapted to cold stress by employing a series of mechanisms to minimize damages caused by exposure to cold temperatures. The molecular mechanisms identified through RNA-Seq included Extracellular matrix (ECM) receptor interaction, glycerolipid metabolism, regulation of autophagy and focal adhesion pathway as playing vital roles in cold tolerance in L. polyactis. This study may help elucidate how L. polyactis tolerates cold, which is of value for breeding cold-tolerant L. polyactis stocks for cultivation.

High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss)

Recently, the research of animal microRNAs (miRNAs) has attracted wide attention for its regulatory effect in the development process and the response to abiotic stresses. Rainbow trout is a commercially and cold water fish species, and usually encounters heat stress, which affects its growth and leads to a huge economic loss. But there were few investigations about the roles of miRNAs in heat stress in rainbow trout. In this study, miRNAs of rainbow trout which were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries from head kidney tissues under control (18 °C) and heat-treated (24 °C) conditions. A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. Ten of these miRNAs were further validated by quantitative real-time PCR. In addition to, including 393 negative correlation miRNA-target gene pairs, several important regulatory pathways were involved in heat stress of the potential target genes, including protein processing in endoplasmic reticulum, NOD-like receptor signaling pathway, and phagosome. Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout, which provide a useful resource for the cultivation of rainbow trout.

iTRAQ-based quantitative proteomic analysis of Takifugu fasciatus liver in response to low-temperature stress

Low temperatures profoundly influence the physiological and behavioural processes of ectotherms, especially teleosts, which have made them the subjects of strong interest over time. However, the characteristics of fish cold-tolerance at the protein level remain unclear. Therefore, to shed further light on the molecular mechanisms of low temperature adaptation in fish, we conducted quantitative proteomics on the T. fasciatus liver using iTRAQ. Comparing the proteomic profiles of the T. fasciatus liver at 12 °C and 26 °C, a total of 3741 proteins were identified, and 160 were differentially abundant proteins (DAPs). Among the DAPs, the most significant changes were noted in proteins involved in oxidative stress (nine proteins), mitochondrial enzymes (eleven proteins) and signal transduction (thirteen proteins). The KEGG enrichment analysis indicated significant enhancement of D-arginine and D-ornithine metabolism, MAPK signalling, Wnt signalling and Gap junction pathway. Subsequently, three significantly up-regulated proteins (CIRB, HSP90 and GST) and two significantly down-regulated proteins (FLNB and A2ML1) were validated with parallel reaction monitoring (PRM) assays. Furthermore, the changes in abundance of proteins that are involved in oxidative stress, mitochondrial enzymes and signal transduction were validated at the transcriptional level with qPCR. These verification results show that the experimental data of iTRAQ are reliable. Our results not only deepen the understanding of the mechanisms underlying low-temperature tolerance in fish, but they also may contribute to the enhancement of cold tolerance during its breeding process. SIGNIFICANCE OF THE STUDY: The study focused on a comparative quantitative proteomics analysis of the T. fasciatus liver in response to low temperatures using iTRAQ, which has not yet been reported in the literatures. The results showed that the effect of low temperature on T. fasciatus is significant, including a detoxification of metabolic by-products and oxidative stress, an activation of the mitochondrial enzyme to strengthen energy metabolism, and a negative effect on signal transduction, which result in dysfunction or suboptimal performance. These low-temperature-related changes in the liver proteome of T. fasciatus can facilitate the understanding of the low temperature-related response that takes place in similar conditions in the liver and may contribute to the breeding of cold-resistant strains.

Network of microRNA-transcriptional factor-mRNA in cold response of turbot Scophthalmus maximus

The aim of this study is to understand fish cold-tolerant mechanism. We analyzed the transcriptional reactions to the cold condition in turbot Scophthalmus maximus by using RNA-seq and microRNA (miRNA)-seq. Meio-gynogenetic diploid turbots were treated at 0 °C to distinguish the cold-tolerant (CT) and cold-sensitive (CS) groups. The results showed that there were quite different responses at both mRNA and miRNA levels, with more up-regulated mRNAs (1069 vs. 194) and less down-regulated miRNAs (4 vs. 1) in CT versus CS relative to the control group. The network of miRNA-transcription factor-mRNA, regulating turbot different response to cold stress, was constructed, which involved in cell cycle, component of cell membrane, signal transduction, and circadian rhythm pathways. The above information demonstrates mechanisms by which cold tolerance is increased in fish.

Transcriptome profiling and histology changes in juvenile blunt snout bream (Megalobrama amblycephala) liver tissue in response to acute thermal stress

To understand the precise mechanism and the pathways activated by thermal stress in fish, we sampled livers from juvenile Megalobrama amblycephala exposed to control (25 °C) and test (35 °C) conditions, and performed short read (100 bp) next-generation RNA sequencing (RNA-seq). Using reads from different temperature, expression analysis identified a total of 440 differentially-expressed genes. These genes were related to oxidative stress, apoptosis, immune responses and so on. We used quantitative real-time reverse transcriptase PCR to assess the differential mRNA expression of selected genes that encode antioxidant enzymes and heat shock proteins in response to thermal stress. Fish exposed to thermal stress also showed liver damage associated with serum biochemical parameter changes. The set of genes identified showed regulatory modulation at different temperatures, and therefore could be further studied to determine how thermal stress damages M. amblycephala livers and the possible roles of reactive oxygen species in this process.

Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus

Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicaudatus using PacBio SMRT Sequencing. A total of 6,918 gene families were identified with two or more isoforms, and 26,683 complete ORFs with an average length of 1,497 bp were detected. Totally, 1,208 high-confidence lncRNAs were identified, and most of these appeared to be precursor transcripts of miRNAs or snoRNAs. Phylogenetic tree of the Misgurnus species was inferred based on the 1,905 single copy orthologous genes. The tetraploid and diploid M. anguillicaudatus grouped into a clade, and M. bipartitus showed a closer relationship with the M. anguillicaudatus. The overall evolutionary rates of tetraploid M. anguillicaudatus were significantly higher than those of other Misgurnus species. Meanwhile, 28 positively selected genes were identified in M. anguillicaudatus clade. These positively selected genes may play critical roles in the adaptation to various habitat environments for M. anguillicaudatus. This study could facilitate further exploration of the genomic signatures of M. anguillicaudatus and provide potential insights into unveiling the evolutionary history of tetraploid loach.

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.

Transcriptome Analysis of Flounder (Paralichthys olivaceus) Gill in Response to Lymphocystis Disease Virus (LCDV) Infection: Novel Insights into Fish Defense Mechanisms

Lymphocystis disease virus (LCDV) infection may induce a variety of host gene expression changes associated with disease development; however, our understanding of the molecular mechanisms underlying host-virus interactions is limited. In this study, RNA sequencing (RNA-seq) was employed to investigate differentially expressed genes (DEGs) in the gill of the flounder (Paralichthys olivaceus) at one week post LCDV infection. Transcriptome sequencing of the gill with and without LCDV infection was performed using the Illumina HiSeq 2500 platform. In total, RNA-seq analysis generated 193,225,170 clean reads aligned with 106,293 unigenes. Among them, 1812 genes were up-regulated and 1626 genes were down-regulated after LCDV infection. The DEGs related to cellular process and metabolism occupied the dominant position involved in the LCDV infection. A further function analysis demonstrated that the genes related to inflammation, the ubiquitin-proteasome pathway, cell proliferation, apoptosis, tumor formation, and anti-viral defense showed a differential expression. Several DEGs including β actin, toll-like receptors, cytokine-related genes, antiviral related genes, and apoptosis related genes were involved in LCDV entry and immune response. In addition, RNA-seq data was validated by quantitative real-time PCR. For the first time, the comprehensive gene expression study provided valuable insights into the host-pathogen interaction between flounder and LCDV.

Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans

Background

False kelpfish (Sebastiscus marmoratus) is one of the target species in artificial breeding in China, and is susceptible to infection by Cryptocaryon irritans, which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of S. marmoratus against C. irritans infection.

Methods

We carried out an extensive analysis of the transcriptome of S. marmoratus immune-related tissues. A paired-end library was constructed from the cDNA synthesized using a Genomic Sample Prep Kit. Five normalized cDNA libraries were constructed using RNA from the control group and the four groups of C. irritans-infected fish. The libraries were sequenced on an Illumina Mi-Seq platform, and functional annotation of the transcriptome was performed using bioinformatics software.

Results

The data produced a total of 149,983,397 clean reads from five cDNA libraries constructed from S. marmoratus immune-related tissues. A total of 33,291 unigenes were assembled with an average length of 1768 bp. In eggNOG (Evolutionary Genealogy of Genes: non-supervised orthologous groups) categories, 333 unigenes (0.94%) were assigned to defense mechanisms. In the immune system process sub-categories of gene ontology (GO) enrichment analysis, with the passage of time post-infection, the number of differentially expressed genes (DEGs) was reduced from 24 h to 48 h but then increased from 72 h to 96 h. Specifically, the immune-related differentially expressed genes (IRDEGs), which belong to the KEGG (Kyoto encyclopedia of genes and genomes) pathways, such as the complement and coagulation cascades, chemokine signalling pathways and toll-like receptor signalling pathways were mainly observed at 24 h post-infection.

Conclusions

Infection with C. irritans resulted in a large number of DEGs in the immune-related tissues of S. marmoratus. The rapid and significant response of the S. marmoratus immune signalling pathways following C. irritans infection may be associated with their involvement in the immune process.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2508-7) contains supplementary material, which is available to authorized users.

Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish

Environmental acclimation is important episode in wildlife occupation of the high-altitude Tibetan Plateau (TP). Transcriptome-wide studies on thermal acclimation mechanism in fish species are rarely revealed in Tibetan Plateau fish at high altitude. Thus, we used mRNA and miRNA transcriptome sequencing to investigate regulation of thermal acclimation in larval Tibetan naked carp, Gymnocypris przewalskii. We first remodeled the regulation network of mRNA and miRNA in thermal acclimation, and then identified differential expression of miRNAs and target mRNAs enriched in metabolic and digestive pathways. Interestingly, we identified two candidate genes contributed to normal skeletal development. The altered expression of these gene groups could potentially be associated with the developmental issues of deformity and induced larval death. Our results have three important implications: first, these findings provide strong evidences to support our hypothesis that G. przewalskii possess ability to build heat-tolerance against the controversial issue. Second, this study shows that transcriptional and post-transcriptional regulations are extensively involved in thermal acclimation. Third, the integrated mRNA and microRNA transcriptome analyses provide a large number of valuable genetic resources for future studies on environmental stress response in G. przewalskii and as a case study in Tibetan Schizothoracine fish.

Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production

Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.

Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus)

The geographic distribution of three Misgurnus species, M. anguillicaudatus, M. bipartitus, and M. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genus Misgurnus. In total, 51 orphan genes (19 in M. anguillicaudatus, 18 in M. bipartitus, and 14 in M. mohoity) that may contribute to the species-specific adaptations were identified. An analysis of 1392 one-to-one orthologous genes revealed significantly higher ratios of nonsynonymous-to-synonymous substitutions in the M. mohoity lineage than in M. anguillicaudatus. The genes displaying signatures of positive selection and rapid evolution in Misgurnus were involved in four function categories, (1) energy metabolism; (2) signal transduction; (3) membrane; and (4) cell proliferation or apoptosis, implying that these candidate genes play critical roles in the thermal adaptation of the fish to their living environments. We also detected more than five positively selected sites in cldn15lb and isca1, which function as important factors in paracellular Na⁺ transport and Fe/S cluster assembly, respectively. Overall, our study provides valuable insights into the adaptive evolution of loaches from different temperature zones in China and is a foundation for future studies to clarify the genetic basis of temperature adaptation in fishes.

Transcriptome analysis of dormant tomonts of the marine fish ectoparasitic ciliate Cryptocaryon irritans under low temperature

BACKGROUND

Cryptocaryon irritans, a species of obligatory ciliate ectoparasite, can infect various species of marine teleost fish. Cryptocaryon irritans that fall to the seabed or aquarium bottom in winter can form "dormant tomonts" and wake up when the temperature rises the next year. Abundant studies and analyses on the dormant tomonts were carried out at the transcriptome level, in order to investigate the molecular mechanism of C. irritans tomonts entering the dormant state under low-temperature conditions.

METHODS

The paired-end sequencing strategy was used to better assemble the entire transcriptome de novo. All clean sequencing reads from each of the three libraries (Group A: untreated blank control; Group B: treated for 24 h at 12 °C; and Group C: developed for 24 h at 25 °C) were respectively mapped back to the transcriptome assembly using the bioinformatics software.

RESULTS

In this study, 25,695,034, 21,944,467, and 28,722,875 paired-end clean reads were obtained respectively from the three cDNA libraries of the C. irritans tomont by Illumina paired-end sequencing technology. A total of 25,925 unique transcript fragments (unigenes) were assembled, with an average length of 839 bp. Differentially expressed genes (DEGs) were scrutinized; in Group B/A pairwise comparison, 343 genes presented differential expression, including 265 up-regulated genes and 78 down-regulated genes in Group B; in Group C/A pairwise comparison, there were 567 DEGs, including 548 up-regulated genes and 19 down-regulated genes in Group C; and in Group B/C pairwise comparison, 185 genes showed differential expression, including 145 up-regulated genes and 40 down-regulated genes in Group B.

CONCLUSIONS

This is the first transcriptomic analytical study of the C. irritans tomonts under low temperature. It can be concluded that most of the genes required for its cell survival under low temperature, or for cell entry into a deeper dormancy state were discovered, and that they might be considered as candidate genes to develop the diagnostic and control measures for cryptocaryoniasis.

Transcriptome and analysis on the complement and coagulation cascades pathway of large yellow croaker (Larimichthys crocea) to ciliate ectoparasite Cryptocaryon irritans infection

Large yellow croaker (Larimichthys crocea) is one of the most valuable marine fish in southern China. Given to the rapid development of aquaculture industry, the L. crocea was subjected to ciliate ectoparasite Cryptocaryon irritans. It therefore is indispensable and urgent to understand the mechanism of L. crocea host defense against C. irritans infection. In the present study, the extensively analysis at the transcriptome level for Cryptocaryoniasis in L. crocea was carried out. These results showed that 15,826,911, 16,462,921, and 15,625,433 paired-end clean reads were obtained from three cDNA libraries (A: 0 theronts/fish, B: 12,000 theronts/fish, and C: 24,000 theronts/fish) of the L. crocea immune-related tissues by Illumina paired-end sequencing technology. Totally, 30,509 unique transcript fragments (unigenes) were assembled, with an average length of 1715 bp. In B/A, C/A, and C/B pairwise comparison, 972, 900, and 1126 genes showed differential expression respectively. Differently expressed immune-related genes (DEIGs) were scrutinized, in B/A pairwise comparison, 48 genes showed differential expression, including 26 up-regulated genes and 22 down-regulated genes in B; in C/A pairwise comparison, there were 39 DEIGs, including 7 up-regulated genes and 32 down-regulated genes in C; in C/B pairwise comparison, 40 genes showed differential expression, including 11 up-regulated genes and 29 down-regulated genes in C. There were 16 DEIGs enriched KEGG pathways, in which the complement and coagulation cascades pathway was the top most DEIGs enriched pathway (B:A = 42; C:A = 28; C:B = 42). The coagulation and fibrinolytic system was in a highly active state after infected by C. irritans with non-lethal concentration; the alternative complement pathway may play an important role in the early stages of C. irritans infection. These results demonstrated that low-concentration infection can significantly induce the immunological response in fishes, however, when fishes were in fatal conditions, the immunity was suppressed.