RNA-Seq technology and its application in fish transcriptomics

Advanced genomic research in understanding fish-borne zoonotic parasitic infection

Fish-borne zoonotic parasites pose substantial risks to human health and global aquaculture, primarily through raw or undercooked fish consumption. The rapid expansion of aquaculture, increasing global fish trade, and rising human populations have amplified these concerns. Despite widespread awareness of meat-borne zoonoses, fish-borne parasitic infections remain underrecognized, especially in developed countries. Traditional morphological and molecular methods have provided critical foundations for studying these parasites, yet recent genomic advances have revolutionized our understanding of their genetic diversity, biology, and host-pathogen dynamics. This review underscores the significance of integrating genomic approaches with conventional methods to enhance disease surveillance, risk assessment, and control strategies. Harnessing genomic tools will enable the development of effective interventions to mitigate zoonotic parasite impacts, protect human health, and promote sustainable aquaculture. A comprehensive, genomics-driven approach is essential to overcoming the global challenges of fish-borne zoonotic infections.

Transcriptomic and biometric parameters analysis in rainbow trout (Oncorhynchus mykiss) challenged with viral hemorrhagic septicemia virus (VHSV)

BACKGROUND

Viral hemorrhagic septicemia virus (VHSV) is a highly pathogenic virus that poses a significant threat to the health of diverse marine species. Among these, trout species, particularly rainbow trout (Oncorhynchus mykiss), are highly susceptible. This study evaluated the effects of VHSV infection on the biometric traits of rainbow trout and investigated the molecular mechanisms associated with the disease.

RESULTS

Biometric traits of fish were collected and documented weekly during the fourth and fifth weeks of the experiment. A statistically significant difference in body weight was observed in the fifth week, particularly between the control group and the groups injected with either physiological saline or the virus. Additionally, body length-related attributes showed significant variation across all treatment groups within the designated timeframe. RNA was extracted from spleen tissue of the group injected with high doses of physiological saline and the group injected with high doses of the virus using the TRIzol protocol. Differential gene expression analysis revealed 1,726 genes with significant differences between the two groups. Several key immune-related genes were identified, including TLR2, TLR7, TLR8, TLR22, IRF5, IRF6, IRF7, IRF8, IRF10, IL11a, IL12B, IL1b, IL7R, ILR1 II, HSP90B1, HSP47, TNF-α, TRF3, SPRY1, CASP3, FN1, GAPDH, and IgGFc-binding proteins. Network-based analysis of differentially expressed genes was conducted using the GeneMANIA module in Cytoscape, and metabolic pathways were identified through the DAVID database. The results highlighted the involvement of key pathways, including the Toll-like receptor pathway, p53 signaling pathway, PPAR signaling pathway, and the cell cycle, in the infected group. Validation tests for selected upregulated (EPCAM, APOC2 and XDD4) and downregulated (TLR7, XDH, and TSPAN36) candidate genes, were conducted using qRT-PCR. The qPCR results showed a strong and statistically significant correlation with the RNA-seq data, confirming the reliability of the findings.

CONCLUSIONS

VHSV significantly impacts the growth of rainbow trout, affecting both body length and gene expression. This study underscores the substantial economic risks posed by the virus and the absence of an effective cure, highlighting the importance of preventative measures. Additionally, potential resistance genes and pathways were identified through RNA sequencing, providing valuable insights for improving trout breeding programs.

Transcriptomic analysis of immune-related genes in Pacific white snook (Centropomus viridis) gills infected with the monogenean parasite Rhabdosynochus viridisi

The parasite Rhabdosynochus viridisi (Platyhelminthes: Monogenea) infects the Pacific white snook Centropomus viridis gills and can cause adverse effects in the aquaculture industry. The immune responses of Pacific white snook to monogenean infections are poorly understood. Thus, this study aimed to identify differentially expressed genes (DEGs) in the gills of Pacific white snook juveniles experimentally infected with R. viridisi, emphasizing immune-related genes and pathways activated or suppressed during the infection. RNA sequencing was performed on the gills of uninfected (control) and infected fish. The algorithm Seq2Fun was selected without a reference transcriptome to map the reads to transcripts of fishes available from a database for gene orthologs (EcoOmics) and obtain the counting table. The ExpressAnalyst software was used for differential expression and functional analyses. A total of 20,106 transcripts were found, and 1430 (7 %) were differentially expressed genes (DEGs) between infected and control groups. We identified 860 (60 %) downregulated and 570 (40 %) upregulated genes. Thirteen canonical pathways after the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were overrepresented, and most of the DEGs were downregulated, suggesting the inactivation of these pathways. The functions of most of the DEGs with higher fold change found in this study are poorly understood in fish. Even though the well-known pro-inflammatory cytokines remained unchanged in infected gills of C. viridis, and transforming growth factor β (tgfβ) was downregulated, interleukin-17 ligands il17d and il17a/f1, as well as C-X-C motif chemokine receptor 2 (cxcr2) genes were upregulated, indicating that the infection with R. viridisi promotes Th17-like immunity. Overexpression of plasma B cell activity markers such as immunoglobulin light chain-like genes and the v-set pre-B cell surrogate light chain 3 (vpreb3) was also detected in this study. The possible implications of DEGs related to calcium imbalance, hypoxia adaptation, hemostasis, and immunity are discussed. These results will support future studies to improve the prevention and treatment of monogenean infections in finfish aquaculture.

Alternative Splicing Events and Differently Expressed Genes During Peak Mortality in Large Yellow Croaker (Larimichthys crocea) Infected with Scuticociliate

Large yellow croaker (Larimichthys crocea) is facing various threats from bacterial, viral, and parasitic diseases, especially scuticociliate. Scuticociliate is a facultative parasite causing high mortality in various marine fishes. In this study, an artificial scuticociliate infection model was successfully established for large yellow croaker. Comparative transcriptome analysis was performed on gill tissues collected from control fish and fish at the peak of mortality following exposure to the parasite to investigate the underlying molecular mechanisms of host-parasite interactions. A total of 400, 427, and 311 differential alternative splicing (DAS) events were identified at 7 d/0 h, 8 d/0 h, and 9 d/0 h, respectively. Meanwhile, 761 differentially expressed genes (DEGs) were found, with 154 simultaneously at three time points. GO and KEGG enrichment analysis showed that DAS genes and DEGs were mainly focused on self-respire, immune, and metabolic-related pathways. The DEGs related to blood coagulation included fga, fgb, fgg, and lectin domain genes. Lectin domain genes were also involved in reducing parasite burden. Cytokines, Caspase-1, trim13, trim16, and trim39 co-participated in immune response. Notably, the complement component gene c3 was both a DEG and underwent DAS. Using STRING software, interaction regulatory networks were constructed to visualize potential hub genes, revealing 22 DEGs shared across at least two time points. These findings provide valuable insights into the immune and metabolic responses of large yellow croaker to scuticociliate infection, offering a foundational reference for identifying resistant genes and understanding fish-parasite interactions.

Experimental reporting of fish transcriptomic responses in environmental toxicology and ecotoxicology

Due to its increasing affordability and efforts to understand transcriptional responses of organisms to biotic and abiotic stimuli, transcriptomics has become an important tool with significant impact on toxicological investigations and hazard and risk assessments, especially during development and application of new approach methodologies (NAMs). Data generated using transcriptomic methodologies have directly informed adverse outcome pathway frameworks, chemical and biological read across, and aided in the identification of points of departure. Using data reporting frameworks for transcriptomics data offers improved transparency and reproducibility of research and an opportunity to identify barriers to adoption of these NAMs, especially in environmental toxicology and ecotoxicology with aquatic models. Improved reporting also allows for reexamination of existing data, limiting needs for experiment replication and further reducing animal experimentation. Here, we use a standardized form of data reporting for omics-based studies, the Organisation for Economic Co-operation and Development omics reporting framework, which specifically reports on a list of parameters that should be included in transcriptomics studies used in a regulatory context. We focused specifically on fish studies using RNA- Sequencing (Seq)/microarray technologies within a toxicology context. Inconsistencies in reporting and methodologies among the experimental designs (toxicology vs. molecular characterization) were observed in addition to foundational differences in reporting of sample concentration or preparation or quality assessments, which can affect reproducibility and read across, confidence in results, and contribute substantially to understanding molecular mechanisms of toxicants and toxins. Our findings present an opportunity for improved research reporting. We also provide several recommendations as logical steps to reduce barriers to adoption of transcriptomics within environmental toxicology and ecotoxicology.

Integrated metabolomic and transcriptomic analysis reveals variation in the metabolites of Dendrobium officinale, Dendrobium huoshanense, Dendrobium nobile

INTRODUCTION

Dendrobium is a perennial herb of the genus Dendrobium in the orchid family. Generally, Dendrobium officinale (TP) and Dendrobium huoshanense (HS) are both considered to have the function of yin-nourishing, while Dendrobium nobile (JC) has better efficacy of heat-clearing. However, because of the wide variety of Dendrobium species, the classification and clinical application of Dendrobium are often confused clearly distinguished in different medicinal uses.

OBJECTIVE

In order to compare the differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) of the three Dendrobium.

METHODS

We selected TP, HS, and JC cultivated on stone for metabolomic and transcriptomic analyses between 2 and 3 years.

RESULTS

The results showed that a total of 489 metabolites were obtained, including 72 were DAMs. The 72 DAMs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. Transcriptome analysis results showed that 1,038 annotated DEGs were identified among the three Dendrobium species. The comprehensive analysis showed that the three Dendrobium differed in the distribution of the content of four major active components: flavonoids, amino acids, alkaloids, and sugars and alcohols, among which the DAMs and DEGs were mainly enriched in metabolic pathways and secondary metabolite biosynthesis.

CONCLUSION

In this study, metabolomics and transcriptomics were utilized to compare the differences among the three species of Dendrobium, to provide theoretical references for future research and selection of different species of Dendrobium based on different medicinal uses, and to lay the foundation for further research on the biosynthesis of flavonoids in Dendrobium.

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.

Analysis of Differential Alternative Splicing in Largemouth Bass After High Temperature Exposure

Temperature is one of the critical factors affecting the physiological functions of fish. With ongoing global warming, changes in water temperature have a profound impact on fish species. Alternative splicing, being a significant mechanism for gene expression regulation, facilitates fish to adapt and thrive in dynamic and varied aquatic environments. Our study used transcriptome sequencing to analyze alternative splicing in largemouth bass gills at 34 °C for 24 h. The findings indicated an increase in both alternative splicing events and alternative splicing genes after high temperature treatment. Specifically, the comparative analysis revealed a total of 674 differential alternative splicing events and 517 differential alternative splicing genes. Enrichment analysis of differential alternative splicing genes revealed significant associations with various gene ontology (GO) terms and KEGG pathways, particularly in immune-related pathways like necroptosis, apoptosis, and the C-type lectin receptor signaling pathway. These results emphasize that some RNA splicing-related genes are involved in the response of largemouth bass to high temperatures.

Silver nanoparticles exhibit ecotoxicological effects via oxidative stress, inflammation, and reproductive toxicity in Asian clam (Corbicula fluminea)

Silver nanoparticles (AgNPs) are pervasive environmental pollutants capable of inducing toxicological impacts on benthic organisms. In this study, the effects of AgNPs on the antioxidant enzyme activities, tissue damage, inflammatory responses, and reproductive toxicity of Corbicula fluminea were investigated. C. fluminea was exposed to four concentrations of AgNPs (0, 5 mg/L, 10 mg/L, and 125 mg/L) for 48 h. The results showed that the higher concentrations of AgNPs caused severe tissue damage in multiple organs of C. fluminea, induced oxidative stress and an imbalance of the antioxidant enzyme activities (such as SOD, CAT, MDA), and increased the inflammatory immune response involving NFκB, TLR2/4, HSP70/90, IL1β, and TNFα. Notably, further transmission electron microscopy and cytological analyses revealed that AgNPs exposure induced apoptosis in the gonad tissues, resulting in significant loss and damage in the oocytes and spermatids. The present study demonstrates the ecotoxicological impacts of AgNPs on freshwater bivalves, particularly highlighting their reproductive toxicity on germ cells, signifying the potential toxic effects of heavy metal pollution on aquatic ecosystems.

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

Identification of Single-Nucleotide Polymorphisms in Differentially Expressed Genes Favoring Soybean Meal Tolerance in Higher-Growth Zebrafish (Danio rerio)

Genetic variability within the same fish species could confer soybean meal (SBM) tolerance in some individuals, thus favoring growth. This study investigates the single-nucleotide polymorphisms (SNPs) in differentially expressed genes (DEGs) favoring SBM tolerance in higher-growth zebrafish (Danio rerio). In a previous work, nineteen families of zebrafish were fed a fish meal diet (100FM control diet) or SBM-based diets supplemented with saponin (50SBM + 2SPN-experimental diet), from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (170 ± 18 mg) or lower (76 ± 10 mg) weight gain on 50SBM + 2SPN in relation to 100FM. Intestinal transcriptomic analysis using RNA-seq revealed six hundred and sixty-five differentially expressed genes in higher-growth fish fed 50SBM + 2SPN diet. In this work, using these results, 47 SNPs in DEGs were selected. These SNPs were genotyped by Sequenom in 340 zebrafish that were fed with a 50SBM + 2SPN diet or with 100FM diet. Marker-trait analysis revealed 4 SNPs associated with growth in 3 immunity-related genes (aif1l, arid3c, and cst14b.2) in response to the 50SBM + 2SPN diet (p-value < 0.05). Two SNPs belonging to aif1l y arid3c produce a positive (+19 mg) and negative (-26 mg) effect on fish growth, respectively. These SNPs can be used as markers to improve the early selection of tolerant fish to SBM diet or other plant-based diets. These genes can be used as biomarkers to identify SNPs in commercial fish, thus contributing to the aquaculture sustainability.

Transcriptome analysis of large yellow croaker (Larimichthys crocea) at different growth rates

The unsynchronized growth of the large yellow croaker (Larimichthys crocea), which impacts growth efficiency, poses a challenge for aquaculture practitioners. In our study, juvenile stocks of large yellow croaker were sorted by size after being cultured in offshore cages for 4 months. Subsequently, individuals from both the fast-growing (FG) and slow-growing (SG) groups were sampled for analysis. High-throughput RNA-Seq was employed to identify genes and pathways that are differentially expressed during varying growth rates, which could suggest potential physiological mechanisms that influence growth rate. Our transcriptome analysis identified 382 differentially expressed genes (DEGs), comprising 145 upregulated and 237 downregulated genes in comparison to the SG group. GO and KEGG enrichment analyses indicated that these DEGs are predominantly involved in signal transduction and biochemical metabolic pathways. Quantitative PCR (qPCR) results demonstrated that cat, fasn, idh1, pgd, fgf19, igf2, and fads2 exhibited higher expression levels, whereas gadd45b and gadd45g showed lower expression compared to the slow-growing group. In conclusion, the differential growth rates of large yellow croaker are intricately associated with cellular proliferation, metabolic rates of the organism, and immune regulation. These findings offer novel insights into the molecular mechanisms and regulatory aspects of growth in large yellow croaker and enhance our understanding of growth-related genes.

Metabolomics in sturgeon research: a mini-review

Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as "living fossils" and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts.

Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms

The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.

Effects of Low-Lipid Diets on Growth, Haematology, Histology and Immune Responses of Parr-Stage Atlantic Salmon (Salmo salar)

Lipids in fish diets provide energy and play important roles in immunity and metabolism. Atlantic salmon, a species that migrates from freshwater to seawater, requires high energy, especially during smoltification. Juvenile teleosts have low lipid requirements, and a high dietary lipid content is known to have negative effects on their growth and digestion. Therefore, this study evaluated the effect of two commercial rainbow trout feeds (low-lipid, 13.41% and 14.6%) on the growth and immune responses of early parr-stage Atlantic salmon compared to commercial salmon feed (high-lipid, 29.52%). Atlantic salmon parr (weight: 14.56 ± 2.1 g; length: 11.23 ± 0.44 cm) were randomly divided into three groups and fed either one of two commercial rainbow trout feeds (RTF1 and RTF2) or the commercial salmon feed (ASF) for 12 weeks. At the end of the feeding trial, growth, haematology, histology and gene expression analyses were performed. There were no significant differences in weight gain rates or feed efficiency between the groups (p > 0.05). Superoxidate dismutase, glutathione peroxidase, lysozyme and immunoglobulin M activities were not different among the experimental groups (p > 0.05). A histological examination of the liver and intestinal tissues showed no pathological symptoms of inflammatory response or lipid accumulation in any of the groups. In an intestinal transcriptome analysis using RNA-seq, the expression levels of several genes linked to lipids, immune-related proteins, cytokines and chemokines did not differ significantly between the groups (p > 0.05). Commercial rainbow trout feed with low lipid content has no clear negative impact on the development of Atlantic salmon during the early parr stage (14.5 to 39.6 g). This study provides basic information for the development of economical feed for early parr-stage Atlantic salmon.

Toxic responses of environmental concentrations of bifenthrin in larval freshwater snail Bellamya aeruginosa

Bifenthrin (BF) is ubiquitous in aquatic environments, and studies have indicated that environmental concentrations of BF could cause neurotoxicity and oxidative damage in fish and decrease the abundance of aquatic insects. However, little information is available on the toxicity of BF in freshwater benthic mollusks. Bellamya aeruginosa (B. aeruginosa) is a key benthic fauna species in aquatic ecosystems, and has extremely high economic and ecological values. In this study, larval B. aeruginosa within 24 h of birth were exposed to 0, 30 or 300 ng/L of BF for 30 days, and then the toxic effects from molecular to individual levels were comprehensively evaluated in all the three treatment groups. It was found that BF at 300 ng/L caused the mortality of snails. Furthermore, BF affected snail behaviors, evidenced by reduced crawling distance and crawling speed. The hepatopancreas of snails in the two BF exposure groups showed significant pathological changes, including increase in the number of yellow granules and occurrence of hemocyte infiltration, epithelial cell thinning, and necrosis. The levels of ROS and MDA were significantly increased after exposure to 300 ng/L BF, and the activities of two antioxidant enzymes SOD and CAT were increased significantly. GSH content decreased significantly after BF exposure, indicating the occurrence of oxidative damage in snails. Transcriptomic results showed that differentially expressed genes (DEGs) were significantly enriched in pathways related to metabolism and neurotoxicity (e.g., oxidative phosphorylation and Parkinson disease), and these results were consistent with those in individual and biochemical levels above. The study indicates that environmental concentration of BF results in decreased survival rates, sluggish behavior, histopathological lesions, oxidative damage, and transcriptomic changes in the larvae of B. aeruginosa. Thus, exposure of larval snails to BF in the wild at concentrations similar to those used in this study might have adverse consequences at the population level. These findings provide a theoretical basis for further assessing the ecological risk of BF to aquatic gastropods.

Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration

Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.

Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics

Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.

Transcriptomic analysis of large yellow croaker (Larimichthys crocea) reveals the suppression of the inflammatory response from Cryptocaryon irritans infection

Large yellow croaker (Larimichthys crocea) is the most productive marine fish in China. Cryptocaryon irritans is an extremely destructive parasite that causes great economic losses in large yellow croaker aquaculture industry. Therefore, it is very necessary to study the immune response of large yellow croaker in response to C. irritans infection. In this study, the transcriptomic profiles of large yellow croaker were sequenced and analyzed in the brain and head kidney at 72 h after C. irritans infection. Cytokines and chemokines related terms were significantly enriched based on the GO enrichment of down-regulated differentially expressed genes (DEGs) from the head kidney. Meanwhile, cytokine-cytokine receptor interaction was significantly enriched based on the KEGG enrichment of up-regulated DEGs from the brain and down-regulated DEGs from the head kidney, respectively. Moreover, the majority of inflammation-related DEGs were significantly up-regulated in the brain, but distinctly down-regulated in the head kidney. These results showed that the brain and head kidney might play different roles against C. irritans infection, and the inflammatory response of large yellow croaker may be restrained during C. irritans infection. Taken together, the transcriptomic analyses will be helpful to more comprehensively understand the immune mechanism of teleost against C. irritans infection, and provide a theoretical basis for the prevention and treatment of Cryptosporidiosis.

Genomics and transcriptomics of the Chinese mitten crabs (Eriocheir sinensis)

To gain a deeper understanding of the genetic factors influencing the growth and development of Eriocheir sinensis, a well-known species of hairy crab found in Yangcheng Lake, this study focused on the de novo genome and full-length transcriptome information of the selected subjects. Specifically, Yangcheng Lake hairy crabs were chosen as the experimental samples. Initially, a genome analysis was performed, resulting in the identification of gene fragments with a combined length of 1266,092,319 bp. Subsequently, a transcriptome analysis was conducted on a mixture of tissues from four different sites, namely muscle, brain, eye, and heart, to further investigate the genetic characteristics at the transcriptome level. The Pacific Biosciences (Pacio) single-molecule real-time sequencing system generated a total of 36.93 G sub-fragments and 175,90041 effective inserts. This research contributes to the indirect comprehension of genetic variations underlying individual traits. Furthermore, a comparison of the obtained data with relevant literature emphasizes the advantages of this study and establishes a basis for further investigations on the Chinese mitten crab.

PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish

Sinocyclocheilus multipunctatus is a second-class nationally protected wild animal in China. As one of the cavefish, S. multipunctatus has strong adaptability to harsh subterranean environments. In this study, we used PacBio SMRT sequencing technology to generate a first representative full-length transcriptome for S. multipunctatus. Sequence clustering analysis obtained 232,126 full-length transcripts. Among all transcripts, 40,487 were annotated in public databases, while 70,300 microsatellites, 2384 transcription factors, and 16,321 long non-coding RNAs were identified. The phylogenetic tree showed that S. multipunctatus shows a closer relationship to Carassius auratus and Cyprinus carpio, phylogenetically diverging from the common ancestor ~14.74 million years ago (Mya). We also found that between 15.6 and 17.5 Mya, S. multipunctatus also experienced an additional whole-genome duplication (WGD) event, which may have promoted the species evolution of S. multipunctatus. Meanwhile, the overall rates of evolutionary of polyploid S. multipunctatus were significantly higher than those of the other cyprinids, and 220 positively selected genes (PSGs) were identified in two sub-genomes of S. multipunctatus. These PSGs are likely to fulfill critical roles in the process of adapting to diverse cave environments. This study has the potential to facilitate future investigations into the genomic characteristics of S. multipunctatus and provide valuable insights into revealing the evolutionary history of polyploid S. multipunctatus.

Hypoxia-induced physiological responses in fish: From organism to tissue to molecular levels

Dissolved oxygen (DO) in water bodies is a prerequisite for fish survival and plays a crucial role in fish growth, development, and physiological processes. However, with increasing eutrophication, greenhouse effects, and extreme weather conditions, DO levels in aquatic environments often become lower than normal. This leads to stress in fish, causing them to exhibit escape behavior, inhibits their growth and development, and causes tissue damage. Moreover, oxidative stress, decreased immune function, and altered metabolism have been observed. Severe hypoxia can cause massive fish mortality, resulting in significant economic losses to the aquaculture industry. In response to hypoxia, fish exhibit a series of behavioral and physiological changes that are self-protective mechanisms formed through long-term evolution. This review summarizes the effects of hypoxic stress on fish, including the asphyxiation point, behavior, growth and reproduction, tissue structure, physiological and biochemical processes, and regulation of gene expression. Furthermore, future research directions are discussed to provide new insights and references.

Anemonefishes: A model system for evolutionary genomics

Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.

LUNCRW: Prediction of potential lncRNA-disease associations based on unbalanced neighborhood constraint random walk

Accumulating evidence suggests that long non-coding RNAs (lncRNAs) are associated with various complex human diseases. They can serve as disease biomarkers and hold considerable promise for the prevention and treatment of various diseases. The traditional random walk algorithms generally exclude the effect of non-neighboring nodes on random walking. In order to overcome the issue, the neighborhood constraint (NC) approach is proposed in this study for regulating the direction of the random walk by computing the effects of both neighboring nodes and non-neighboring nodes. Then the association matrix is updated by matrix multiplication for minimizing the effect of the false negative data. The heterogeneous lncRNA-disease network is finally analyzed using an unbalanced random walk method for predicting the potential lncRNA-disease associations. The LUNCRW model is therefore developed for predicting potential lncRNA-disease associations. The area under the curve (AUC) values of the LUNCRW model in leave-one-out cross-validation and five-fold cross-validation were 0.951 and 0.9486 ± 0.0011, respectively. Data from published case studies on three diseases, including squamous cell carcinoma, hepatocellular carcinoma, and renal cell carcinoma, confirmed the predictive potential of the LUNCRW model. Altogether, the findings indicated that the performance of the LUNCRW method is superior to that of existing methods in predicting potential lncRNA-disease associations.

Investigating the Mechanism of Low-Salinity Environmental Adaptation in Sepia esculenta Larvae through Transcriptome Profiling

Sepia esculenta is an economically important mollusk distributed in the coastal waters of China. Juveniles are more susceptible to stimulation by the external environment than mature individuals. The ocean salinity fluctuates due to environmental changes. However, there is a lack of research on the salinity adaptations of S. esculenta. Therefore, in this study, we investigated the differential expression of genes in S. esculenta larvae after stimulation by low salinity. RNA samples were sequenced and 1039 differentially expressed genes (DEGs) were identified. Then, enrichment analysis was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Finally, a protein-protein interaction network (PPI) was constructed, and the functions of key genes in S. esculenta larvae after low-salinity stimulation were explored. We suggest that low salinity leads to an excess proliferation of cells in S. esculenta larvae that, in turn, affects normal physiological activities. The results of this study can aid in the artificial incubation of S. esculenta and reduce the mortality of larvae.

Regulation of omega-3 fatty acids production by different genes in freshwater fish species: a review

The present study aims to compare the gene expression of three different fish species (common carp, tilapia, and trout) with varying levels of fatty acids (FA). Based on transcriptome analysis and RNA sequencing, various genes and their associated metabolic pathways are identified. Pathways are categorized based on the genes they encode. Genes that were differentially expressed and their promoter's methylation patterns were revealed by RNA-seq analysis in common carp. Furthermore, fatty acid-enriched pathways, such as ARA4 and adipocytokine signaling, were also identified. Many genes and pathways may influence tilapia's growth and omega-3 content. Using the mTOR pathway, trout with differential expression were discovered to be involved in producing omega-3 fatty acids. This study revealed major pathways in fish species to produce omega-3 fatty acids.

Perfluorohexanesulfonic acid (PFHxS) induces oxidative stress and causes developmental toxicities in zebrafish embryos

Perfluorohexanesulfonic acid (PFHxS) is a short-chain perfluoroalkyl substance widely used to replace the banned perfluorooctanesulfonic acid (PFOS) in different industrial and household products. It has currently been identified in the environment and human bodies; nonetheless, the possible toxicities are not well-known. Zebrafish have been used as a toxicant screening model due to their fast and transparent developmental processes. In this study, zebrafish embryos were exposed to PFHxS for five days, and various experiments were performed to monitor the developmental and cellular processes. Liquid chromatography-mass spectrometry (LC/MS) analysis confirmed that PFHxS was absorbed and accumulated in the zebrafish embryos. We reported that 2.5 µM or higher PFHxS exposure induced phenotypic abnormalities, marked by developmental delay in the mid-hind brain boundary and yolk sac edema. Additionally, larvae exposed to PFHxS displayed facial malformation due to the reduction of neural crest cell expression. RNA sequencing analysis further identified 4643 differentiated expressed transcripts in 5 µM PFHxS-exposed 5-days post fertilization (5-dpf) larvae. Bioinformatics analysis revealed that glucose metabolism, lipid metabolism, as well as oxidative stress were enriched in the PFHxS-exposed larvae. To validate these findings, a series of biological experiments were conducted. PFHxS exposure led to a nearly 4-fold increase in reactive oxygen species, possibly due to hyperglycemia and impaired glutathione balance. The Oil Red O' staining and qPCR analysis strengthens the notions that lipid metabolism was disrupted, leading to lipid accumulation, lipid peroxidation, and malondialdehyde formation. All these alterations ultimately affected cell cycle events, resulting in S and G2/M cell cycle arrest. In conclusion, our study demonstrated that PFHxS could accumulate and induce various developmental toxicities in aquatic life, and such data might assist the government to accelerate the regulatory policy on PFHxS usage.

RNA-Seq Identified Putative Genes Conferring Photosynthesis and Root Development of Melon under Salt Stress

Melon is an important fruit crop of the Cucurbitaceae family that is being cultivated over a large area in China. Unfortunately, salt stress has crucial effects on crop plants and damages photosynthesis, membranal lipid components, and hormonal metabolism, which leads to metabolic imbalance and retarded growth. Herein, we performed RNA-seq analysis and a physiological parameter evaluation to assess the salt-induced stress impact on photosynthesis and root development activity in melon. The endogenous quantification analysis showed that the significant oxidative damage in the membranal system resulted in an increased ratio of non-bilayer/bilayer lipid (MGDG/DGDG), suggesting severe irregular stability in the photosynthetic membrane. Meanwhile, root development was slowed down by a superoxidized membrane system, and downregulated genes showed significant contributions to cell wall biosynthesis and IAA metabolism. The comparative transcriptomic analysis also exhibited that major DEGs were more common in the intrinsic membrane component, photosynthesis, and metabolism. These are all processes that are usually involved in negative responses. Further, the WGCN analysis revealed the involvement of two main network modules: the thylakoid membrane and proteins related to photosystem II. The qRT-PCR analysis exhibited that two key genes (MELO3C006053.2 and MELO3C023596.2) had significant variations in expression profiling at different time intervals of salt stress treatments (0, 6, 12, 24, and 48 h), which were also consistent with the RNA-seq results, denoting the significant accuracy of molecular dataset analysis. In summary, we performed an extensive molecular and metabolic investigation to check the salt-stress-induced physiological changes in melon and proposed that the PSII reaction centre may likely be the primary stress target.

Exploration of anti-stress mechanisms in high temperature exposed juvenile golden cuttlefish (Sepia esculenta) based on transcriptome profiling

Sepia esculenta is a cephalopod widely distributed in the Western Pacific Ocean, and there has been growing research interest due to its high economic and nutritional value. The limited anti-stress capacity of larvae renders challenges for their adaptation to high ambient temperatures. Exposure to high temperatures produces intense stress responses, thereby affecting survival, metabolism, immunity, and other life activities. Notably, the molecular mechanisms by which larval cuttlefish cope with high temperatures are not well understood. As such, in the present study, transcriptome sequencing of S. esculenta larvae was performed and 1,927 differentially expressed genes (DEGs) were identified. DEGs were subjected to functional enrichment analyses using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The top 20 terms of biological processes in GO and 20 high-temperature stress-related pathways in KEGG functional enrichment analysis were identified. A protein-protein interaction network was constructed to investigate the interaction between temperature stress-related genes. A total of 30 key genes with a high degree of participation in KEGG signaling pathways or protein-protein interactions were identified and subsequently validated using quantitative RT-PCR. Through a comprehensive analysis of the protein-protein interaction network and KEGG signaling pathway, the functions of three hub genes (HSP90AA1, PSMD6, and PSMA5), which belong to the heat shock protein family and proteasome, were explored. The present results can facilitate further understanding of the mechanism of high temperature resistance in invertebrates and provide a reference for the S. esculenta industry in the context of global warming.

Integrated lipidomics and transcriptomics analysis reveal lipid metabolism disturbance in scallop (Chlamys farreri) exposure to benzo[a]pyrene

Benzo[a]pyrene (B[a]P) commonly bioaccumulates in lipid-rich tissues due to its lipophilicity and further affects lipid metabolism. The present study systematically investigated the lipid metabolism disturbance in digestive glands of scallops (Chlamys farreri) exposure to B[a]P, based on lipidomics, transcriptomics, molecular and biochemical analysis. We exposed the scallops to environmentally relevant concentrations of B[a]P for 21 days. The bioaccumulation of B[a]P, lipid content and lipid peroxidation in digestive glands were measured. Integrated lipidomics and transcriptomics analysis, the differential lipid species were identified and key genes based on the pathways in which genes and lipid species involved together were selected in scallop exposure to 10 μg/L B[a]P. The changes of lipid profile showed that triglycerides (TGs) were accumulated after 21 days exposure, while the phospholipids (PLs) decreased demonstrated membrane structures were disrupted by B[a]P. In combination with the change of gene expression, we speculated that B[a]P could induce lipids accumulation by up-regulating lipid synthesis-related genes expression, down-regulating lipolysis-related genes expression and interfering with lipid transport. Overall, this study provides new insights into the mechanisms of lipid metabolism disturbance in bivalves exposed to PAHs, and establishes a foundation for understanding the bioaccumulation mechanism of B[a]P in aquatic organisms, which is of great importance for further ecotoxicological study.

Effect of aging of microplastics on gene expression levels of the marine mussel Mytilus edulis: Comparison in vitro/in vivo exposures

In the present study, effects of aging MPs of polyethylene (PE) were investigated in the marine mussel Mytilus edulis, commonly used as bioindicator of aquatic ecosystem, using both in vitro and in vivo exposures, using concentrations found in marine waters (0.008, 10 and 100 μg.L-1). Changes in gene expression levels implicated in detoxification, immune system, cytoskeletton and cell cycle control were evaluated by quantitative RT-qPCR. Results demonstrated differential expression levels depending upon the state of plastic degradation (aged vs non-aged) and way of exposure (vitro vs vivo). This study highlighted the interest of using molecular biomarkers based on analysis of gene expression pattern in an ecotoxicological context that gives indication of relative slight changes between tested conditions as compared to other biochemical approaches (e.g. enzymatic activities). In addition, in vitro analysis could be used to generate large amount of data as regards to the toxicological effects of MPs.

Different reoxygenation rates induce different metabolic, apoptotic and immune responses in Golden Pompano (Trachinotus blochii) after hypoxic stress

Dissolved oxygen (DO) is essential for teleosts, and fluctuating environmental factors can result in hypoxic stress in the golden pompano (Trachinotus blochii). However, it is unknown whether different recovery speeds of DO concentration after hypoxia induce stress in T. blochii. In this study, T. blochii was subjected to hypoxic conditions (1.9 ± 0.2 mg/L) for 12 h followed by 12 h of reoxygenation at two different speeds (30 mg/L per hour and 1.7 mg/L per hour increasing). The gradual reoxygenation group (GRG), experienced DO recovery (1.9 ± 0.2 to 6.8 ± 0.2 mg/L) within 3 h, and the rapid reoxygenation group (RRG), experienced DO recovery (1.9 ± 0.2 to 6.8 ± 0.2 mg/L) within 10 min. Physiological and biochemical parameters of metabolism (glucose, glycegon, lactic acid (LD), lactate dehydrogenase (LDH), pyruvic acid (PA), phosphofructokinase (PFKA), and hexokinase (HK), triglyceride (TG), lipoprotein lipase (LPL), carnitine palmitoyltransferase 1 (CPT-1)) and transcriptome sequencing (RNA-seq of liver) were monitored to identify the effects of the two reoxygenation speeds. Increased LD content and increased activity of LDH, PA, PFKA, and HK suggested enhanced anaerobic glycolysis under hypoxic stress. LD and LDH levels remained significantly elevated during reoxygenation, indicating that the effects of hypoxia were not immediately alleviated during reoxygenation. The expressions of PGM2, PFKA, GAPDH, and PK were increased in the RRG, which suggests that glycolysis was enhanced. The same pattern was not observed in the GRG. Additionally, In the RRG, reoxygenation may promote glycolysis to guarantee energy supply. However, the GRG may through the lipid metabolism such as steroid biosynthesis at the later stage of reoxygenation. In the aspect of apoptosis, differentially expressed genes (DEGs) in the RRG were enriched in the p53 signaling pathway, which promoted cell apoptosis, while DEGs in the GRG seem to activate cell apoptosis at early stage of reoxygenation but was restrained latterly. DEGs in both the RRG and the GRG were enriched in the NF-kappa B and JAK-STAT signaling pathways, the RRG may induce cell survival by regulating the expression of IL-12B, COX2, and Bcl-XL, while in the GRG it may induce by regulating the expression of IL-8. Moreover, DEGs in the RRG were also enriched in the Toll-like receptor signaling pathway. This research revealed that at different velocity of reoxygenation after hypoxic stress, T. blochii would represent different metabolic, apoptotic and immune strategies, and this conclusion would provide new insight into the response to hypoxia and reoxygenation in teleosts.

Integration of Transcriptomics and Non-Targeted Metabolomics Reveals the Underlying Mechanism of Skeletal Muscle Development in Duck during Embryonic Stage

Skeletal muscle is an important economic trait in duck breeding; however, little is known about the molecular mechanisms of its embryonic development. Here, the transcriptomes and metabolomes of breast muscle of Pekin duck from 15 (E15_BM), 21 (E21_BM), and 27 (E27_BM) days of incubation were compared and analyzed. The metabolome results showed that the differentially accumulated metabolites (DAMs), including the up-regulated metabolites, l-glutamic acid, n-acetyl-1-aspartylglutamic acid, l-2-aminoadipic acid, 3-hydroxybutyric acid, bilirubin, and the significantly down-regulated metabolites, palmitic acid, 4-guanidinobutanoate, myristic acid, 3-dehydroxycarnitine, and s-adenosylmethioninamine, were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of cofactors, protein digestion and absorption, and histidine metabolism, suggesting that these pathways may play important roles in the muscle development of duck during the embryonic stage. Moreover, a total of 2142 (1552 up-regulated and 590 down-regulated), 4873 (3810 up-regulated and 1063 down-regulated), and 2401 (1606 up-regulated and 795 down-regulated) DEGs were identified from E15_BM vs. E21_BM, E15_BM vs. E27_BM and E21_BM vs. E27_BM in the transcriptome, respectively. The significantly enriched GO terms from biological processes were positive regulation of cell proliferation, regulation of cell cycle, actin filament organization, and regulation of actin cytoskeleton organization, which were associated with muscle or cell growth and development. Seven significant pathways, highly enriched by FYN, PTK2, PXN, CRK, CRKL, PAK, RHOA, ROCK, INSR, PDPK1, and ARHGEF, were focal adhesion, regulation of actin cytoskeleton, wnt signaling pathway, insulin signaling pathway, extracellular matrix (ECM)-receptor interaction, cell cycle, and adherens junction, which participated in regulating the development of skeletal muscle in Pekin duck during the embryonic stage. KEGG pathway analysis of the integrated transcriptome and metabolome indicated that the pathways, including arginine and proline metabolism, protein digestion and absorption, and histidine metabolism, were involved in regulating skeletal muscle development in embryonic Pekin duck. These findings suggested that the candidate genes and metabolites involved in crucial biological pathways may regulate muscle development in the Pekin duck at the embryonic stage, and increased our understanding of the molecular mechanisms underlying the avian muscle development.

Transcriptome analyses reveal differentially expressed genes associated with development of the palatal organ in bighead carp (Hypophthalmichthys nobilis)

The palatal organ is a filter-feeding related organ and occupies a considerable proportion of the head of bighead carp (Hypophthalmichthys nobilis), a large cyprinid fish intensive aquaculture in Asia. In this study, we performed RNA-seq of the palatal organ during growth periods of two (M2), six (M6) and 15 (M15) months of age after hatching. The numbers of differentially expressed genes (DEGs) were 1384, 481 and 1837 for M2 VS M6, M6 VS M15 and M2 VS M15 respectively. The following signaling pathways of energy metabolism and cytoskeleton function were enriched, including ECM-receptor interaction, Cardiac muscle contraction, Steroid biosynthesis and PPAR signaling pathway. Several members of collagen family (col1a1, col2a1, col6a2, col6a3, col9a2), Laminin gamma 1 (lamc1), integrin alpha 1 (itga1), Fatty acid binding protein 2 (fads2) and lipoprotein lipase (lpl), and Protein tyrosine kinase 7 (Ptk7) are candidate genes for growth and development of basic tissues of the palatal organ. Furthermore, taste-related genes such as fgfrl1, fgf8a, fsta and notch1a were also identified, which may be involved in the development of taste buds of the palatal organ. The transcriptome data obtained in this study provide insights into the understanding functions and development mechanisms of palatal organ, and potential candidate genes that may be related to the genetic modulation of head size of bighead carp.

Recent advances in predicting lncRNA-disease associations based on computational methods

Mutations in and dysregulation of long non-coding RNAs (lncRNAs) are closely associated with the development of various human complex diseases, but only a few lncRNAs have been experimentally confirmed to be associated with human diseases. Predicting new potential lncRNA-disease associations (LDAs) will help us to understand the pathogenesis of human diseases and to detect disease markers, as well as in disease diagnosis, prevention and treatment. Computational methods can effectively narrow down the screening scope of biological experiments, thereby reducing the duration and cost of such experiments. In this review, we outline recent advances in computational methods for predicting LDAs, focusing on LDA databases, lncRNA/disease similarity calculations, and advanced computational models. In addition, we analyze the limitations of various computational models and discuss future challenges and directions for development.

Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation

RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.

Transcriptome Analysis of Marbled Rockfish Sebastiscus marmoratus under Salinity Stress

The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2,160 were novel genes. Compared to 20‱, 479 and 520 differential genes were obtained for 35‱ and 10‱, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence.

Sex steroid profile during oocyte development and maturation in the intertidal worm Marphysa madrasi (Polychaeta: Eunicidae) from the east coast of India

Marphysa madrasi is a commercially valuable maturation diet in crustacean aquaculture. This study presents the first detailed investigation of oogenesis in the intertidal polychaete worm M. madrasi and reports the steroid profile during oocyte growth and development. Oogenesis is extraovarian type I, originating from coelomic epithelial cells, with four stages of development - primary growth, early vitellogenic, late vitellogenic, and maturation. The primary growth phase contains oogonial cells and previtellogenic oocyte clusters in the early, mid, and late stages of development form a dispersed ovary attached to blood vessels. The late previtellogenic oocytes detach from the ovary at the onset of vitellogenesis. The detached oocytes complete vitellogenesis and final maturation in the coelomic fluid as solitary free-floating cells without any connection with follicle cells. The worms display asynchronous reproduction with a heterogeneous population of developing oocytes. Steroid extracts from the polychaete homogenates in different stages of oogenesis were identified by HPLC and confirmed by LC-MS/MS. In M. madrasi, two vertebrate-type steroids, pregnenolone (P5) and 17α-hydroxyprogesterone (17-OHP) were detected and quantified. The P5 levels were low in immature worms but increased significantly by ∼ 8.3-fold in the previtellogenic stage and peaked during oocyte maturation. 17-OHP levels were low in immature worms but gradually increase as the oogenesis progress to the primary growth and early vitellogenic phase, with a significant increase (p < 0.001) during the late vitellogenic phase. Although an increase in the concentration of P5 and 17-OHP during vitellogenesis and maturation of oocytes points to a possible role in reproduction, the absence of other vertebrate-type steroids in the investigated polychaete signifies a plausible uptake of P5 and 17-OHP from the environment.

Morphological and Molecular Functional Evidence of the Pharyngeal Sac in the Digestive Tract of Silver Pomfret, Pampus argenteus

The pharyngeal sac is a comparatively rare organ in the digestive tract among teleost fishes. However, our understanding of this remarkable organ in the silver pomfret (Pampus argenteus) is limited. In the present study, we examined the various morphological and histological characteristics of the pharyngeal sac using histochemical techniques and electron microscopy. The pharyngeal sac showed unique characteristics such as well-developed muscular walls, weakly keratinized epithelium, numerous goblet cells, and needle-like processes on the papillae. The porous cavity of the papillae contained numerous adipocytes and was tightly enveloped by type I collagen fibers. These structures might provide mechanical protection and excellent biomechanical properties for grinding and shredding prey. A comparison of gene expression levels between the pharyngeal sac and esophagus using RNA-seq showed that phenotype-associated genes (epithelial genes and muscle genes) were upregulated, whereas genes related to nutrient digestion and absorption were downregulated in the pharyngeal sac. These results support the role of the pharyngeal sac in shredding and predigesting food. Overall, these findings provide a clearer understanding of the pharyngeal sac morphology and explain the morphological adaptations of the digestive tract for feeding on gelatinous prey. To our knowledge, this is the first report on pharyngeal sac gene expression in P. argenteus.

Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits

Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.

Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa

The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.

Effects of Dietary Supplementation with Aurantiochytrium sp. on Zebrafish Growth as Determined by Transcriptomics

The marine protist Aurantiochytrium produces several bioactive chemicals, including EPA (eicosapentaenoic acid), DHA (docosahexaenoic acid), and other critical fish fatty acids. It has the potential to improve growth and fatty acid profiles in aquatic taxa. This study evaluated zebrafish growth performance in response to diets containing 1% to 3% Aurantiochytrium sp. crude extract (TE) and single extract for 56 days. Growth performance was best in the 1% TE group, and therefore, this concentration was used for further analyses of the influence of Aurantiochytrium sp. Levels of hepatic lipase, glucose-6-phosphate dehydrogenase, acetyl-CoA oxidase, glutathione peroxidase, and superoxide dismutase increased significantly in response to 1% TE, while malic enzyme activity, carnitine lipid acylase, acetyl-CoA carboxylase, fatty acid synthase, and malondialdehyde levels decreased. These findings suggest that Aurantiochytrium sp. extract can modulate lipase activity, improve lipid synthesis, and decrease oxidative damage caused by lipid peroxidation. Transcriptome analysis revealed 310 genes that were differentially expressed between the 1% TE group and the control group, including 185 up-regulated genes and 125 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses of the differentially expressed genes revealed that Aurantiochytrium sp. extracts may influence liver metabolism, cell proliferation, motility, and signal transduction in zebrafish.

Transgenerational effects of co-exposure to cadmium and carbofuran on zebrafish based on biochemical and transcriptomic analyses

The combined toxicity of heavy metals and pesticides to aquatic organisms is still largely unexplored. In this study, we investigated the combined impacts of cadmium (Cd) and carbofuran (CAR) on female zebrafish (F0 generation) and their following F1 generation. Results showed that mixtures of Cd and CAR induced acute synergistic effects on both zebrafish adults of the F0 generation and embryos of the F1 generation. Combined exposure to Cd and CAR could obviously alter the hepatic VTG level of females, and the individual exposures increased the relative mRNA levels of vtg1 and vtg2. Through maternal transmission, co-exposure of Cd and CAR caused toxicity to 4-day-old larvae of the F1 generation, evidenced by the significant changes in T4 and VTG levels, CYP450 activity, and the relative transcriptional levels of genes related to the hormone, oxidative stress, and apoptosis. These effects were also reflected by the global gene expression pattern to 7-day-old larvae of F1 generation using the transcriptomic analysis, and they could also affect energy metabolism. Our results provided a more comprehensive insight into the transgenerational toxic impacts of heavy metal and pesticide mixtures. These findings highlighted that it was highly necessary to consider transgenerational exposures in the ecological risk assessment of chemical mixtures.

Climate change, human health, and the exposome: Utilizing OMIC technologies to navigate an era of uncertainty

Climate change is an anthropogenic phenomenon that is alarming scientists and non-scientists alike. The emission of greenhouse gases is causing the temperature of the earth to rise and this increase is accompanied by a multitude of climate change-induced environmental exposures with potential health impacts. Tracking human exposure has been a major research interest of scientists worldwide. This has led to the development of exposome studies that examine internal and external individual exposures over their lifetime and correlate them to health. The monitoring of health has also benefited from significant technological advances in the field of "omics" technologies that analyze physiological changes on the nucleic acid, protein, and metabolism levels, among others. In this review, we discuss various climate change-induced environmental exposures and their potential health implications. We also highlight the potential integration of the technological advancements in the fields of exposome tracking, climate monitoring, and omics technologies shedding light on important questions that need to be answered.

Skin transcriptomic analysis and immune-related gene expression of golden pompano (Trachinotus ovatus) after Amyloodinium ocellatum infection

Amyloodiniosis is a severe disease of marine and brackish water fish caused by Amyloodinium ocellatum. Golden pompano (Trachinotus ovatus) is often repeatedly infected by A. ocellatum, leading to extensive mortality. However, little is known about the immune response mechanisms of the T. ovatus following reinfection with A. ocellatum. In this study, an extensive analysis at the transcriptome level of T. ovatus skin was carried out at 24 h post-infection by A. ocellatum. During the transcriptomic analysis, 1367 differentially expressed genes (DEGs) in the skin of T. ovatus under A. ocellatum infection and control conditions were obtained. In Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotated analyses, the DEGs were significantly enriched in the immune-related pathways. To better understand the immune-related gene expression dynamics, a quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was used to assess the primary and secondary infection groups of T. ovatus at different stages (3 h, 12 h, 24 h, 48 h and, 72 h post-infection) of infection with A.ocellatum. The results showed that innate immunity-related genes [interleukin (IL-8), chemokine ligand 3 (CCL3), toll-like receptor 7 (TLR7), and G-type lysosome (LZM g)] and adaptive immunity-related gene [major histocompatibility complex (MHC) alpha antigen I and MHC alpha antigen II] expression levels in the primary and secondary infection groups were significantly increased compared to the control group. The expression of MHC I and MHC II was more rapidly upregulated in the secondary infection group compared with the primary infection group after A.ocellatum infection. However, no significant differences of A.ocellatum load were observed in primary and secondary infection groups. In addition, the serum of the primary infection group had significantly higher concentrations of triglyceride (TG), higher alanine transaminase (ALT), aspartate transaminase (AST), and lactate dehydrogenase (LDH) activities than the control group. This study contributes to understanding the defense mechanisms in fish skin against ectoparasite infection.

Potential biomarkers of endocrine and habitat disruption identified via RNA-Seq in Salvelinus fontinalis with proximity to fracking operations in Pennsylvania headwater stream ecosystems

Unconventional natural gas development (fracking) has been a rapidly expanding technique used for the extraction of natural gas from the Marcellus Shale formation in Pennsylvania. There remains a knowledge gap regarding the ecological impacts of fracking, especially regarding the long-term health of native Brook trout (Salvelinus fontinalis) populations. During the summer of 2015, Brook trout were sampled from twelve streams located in forested, northwestern Pennsylvania in order to evaluate the impacts of fracking on Brook trout. Four stream sites were undisturbed (no fracking activity), three had a developed well pad without fracking activity, and five had active fracking with natural gas production. Liver tissue was isolated from two to five fish per stream and underwent RNA-Seq analysis to identify differentially expressed genes between ecosystems with differing fracking status. Data were analyzed individually and with samples pooled within-stream to account for hierarchical data structure and variation in sample coverage within streams. Differentially expressed and differentially alternatively spliced genes had functions related to lipid and steroid metabolism, mRNA processing, RNA polymerase and protein regulation. Unique to our study, genes related to xenobiotic and stress responses were found as well as potential markers for endocrine disruption and saline adaptation that were identified in watersheds with active fracking activity. These results support the utility of RNA-Seq to assess trout health and suggest detrimental impacts of fracking on sensitive trout populations.

FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species

The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food industry. Furthermore, there is a lack of online platform to analyze users’ new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, including gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, co-expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample information, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.

Aquaculture omics: An update on the current status of research and data analysis

Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.