Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Transcriptome analysis of Macrobrachium rosenbergii hemocytes reveals in-depth insights into the immune response to Vibrio parahaemolyticus infection

Macrobrachium rosenbergii as one of the common freshwater prawn species in Southeast Asia, which breeding industry is seriously threatened by vibriosis and causes high mortality. In this study, the RNA-seq was employed for assessing the M. rosenbergii hemocytes transcriptomes following Vibrio parahaemolyticus challenge. After challenge for 6 h (h), there were overall 1849 DEGs or differentially expressed genes, including 1542 up-regulated and 307 down-regulated genes, and there was a total of 1048 DEGs, including 510 up-regulated genes and 538 down-regulated genes, after challenge for 12 h. Mitogen-activated protein kinase (MAPK) immune-related pathways, Toll, immune deficiency (IMD), and Janus kinase (JAK)/signal transducer and activator of transcription (STAT) were among the immune pathways where a lot of the DEGs were connected. The expression patterns of 18 chosen immune-related genes were examined utilizing qRT-PCR or quantitative real-time polymerase chain reaction, which revealed that the V. parahaemolyticus infection activated the M. rosenbergii's immune response. Permutational multivariate analysis of variance (PERMANOVA) showed that V. parahaemolyticus infection modulated immune regulation and apoptosis pathways. The gathered information provided new insight into M. rosenbergii's immunity and suggested a novel approach to fight against bacterial infection.

Transcriptome, intestinal microbiome and histomorphology profiling of differences in the response of Chinese sea bass (Lateolabrax maculatus) to Aeromonas hydrophila infection

The Chinese sea bass (Lateolabrax maculatus) is an important aquaculture fish, but diseases caused by Aeromonas hydrophila have led to severe economic losses to the aquaculture industry in recent years. To date, only a few studies have focused on the relationship between the intestinal immune response and changes in intestinal microbes by A. hydrophila infection. Here, we report the transcriptome and intestinal changes in infected sea bass. Histopathological results showed that severe steatosis and vacuolation occurred in the liver and that the intestinal villi and mesentery were seriously affected after infection. By extracting total RNA from intestinal tissue and studying the transcriptome profile, 1,678 genes (1,013 upregulated and 665 downregulated) were identified as significantly differentially expressed genes (DEGs). These genes are involved in many immune-related signalling pathways, such as the NOD-like receptor, C-type lectin receptor, and Toll-like receptor signalling pathways. Moreover, the intestinal microbes of sea bass changed significantly after infection. Interestingly, at the genus level, there was an increase in Serratia, Candida arthromitus and Faecalibacterium as well as a decrease in Akkermansia and Parabacteroides after infection. The results also indicated that some of the DEGs involved in the immune response were related to the genus level of intestinal microbiota. Finally, there was a relationship between gene expression patterns and the bacterial structure in the host intestine. Our study provides a reference for the study of the immune response and particular functions of intestinal microbes of sea bass after pathogen infection.

Heat Shock Proteins (Hsps) in Cellular Homeostasis: A Promising Tool for Health Management in Crustacean Aquaculture

Heat shock proteins (Hsps) are a family of ubiquitously expressed stress proteins and extrinsic chaperones that are required for viability and cell growth in all living organisms. These proteins are highly conserved and produced in all cellular organisms when exposed to stress. Hsps play a significant role in protein synthesis and homeostasis, as well as in the maintenance of overall health in crustaceans against various internal and external environmental stresses. Recent reports have suggested that enhancing in vivo Hsp levels via non-lethal heat shock, exogenous Hsps, or plant-based compounds, could be a promising strategy used to develop protective immunity in crustaceans against both abiotic and biotic stresses. Hence, Hsps as the agent of being an immune booster and increasing disease resistance will present a significant advancement in reducing stressful conditions in the aquaculture system.

Functional characterization of Vibrio alginolyticus T3SS regulator ExsA and evaluation of its mutant as a live attenuated vaccine candidate in zebrafish (Danio rerio) model

Vibrio alginolyticus, a Gram-negative bacterium, is an opportunistic pathogen of both marine animals and humans, resulting in significant losses in the aquaculture industry. Type III secretion system (T3SS) is a crucial virulence mechanism of V. alginolyticus. In this study, the T3SS regulatory gene exsA, which was cloned from V. alginolyticus wild-type strain HY9901, is 861 bp encoding a protein of 286 amino acids. The ΔexsA was constructed by homologous recombination and Overlap-PCR. Although there was no difference in growth between HY9901 and ΔexsA, the ΔexsA exhibited significantly decreased extracellular protease activity and biofilm formation. Besides, the ΔexsA showed a weakened swarming phenotype and an ~100-fold decrease in virulence to zebrafish. Antibiotic susceptibility testing showed the HY9901ΔexsA was more sensitive to kanamycin, minocycline, tetracycline, gentamicin, doxycycline and neomycin. Compared to HY9901 there were 541 up-regulated genes and 663 down-regulated genes in ΔexsA, screened by transcriptome sequencing. qRT-PCR and β-galactosidase reporter assays were used to analyze the transcription levels of hop gene revealing that exsA gene could facilitate the expression of hop gene. Finally, Danio rerio, vaccinated with ΔexsA through intramuscular injection, induced a relative percent survival (RPS) value of 66.7% after challenging with HY9901 wild type strain. qRT-PCR assays showed that vaccination with ΔexsA increased the expression of immune-related genes, including GATA-1, IL6, IgM, and TNF-α in zebrafish. In summary, these results demonstrate the importance of exsA in V. alginolyticus and provide a basis for further investigations into the virulence and infection mechanism.

Transcriptome Analysis and Identification of a Female-Specific SSR Marker in Pistacia chinensis Based on Illumina Paired-End RNA Sequencing

Pistacia chinensis Bunge (P. chinensis), a dioecious plant species, has been widely found in China. The female P. chinensis plants are more important than male plants in agricultural production, as their seeds can serve as an ideal feedstock for biodiesel. However, the sex of P. chinensis plants is hard to distinguish during the seedling stage due to the scarcity of available transcriptomic and genomic information. In this work, Illumina paired-end RNA sequencing assay was conducted to unravel the transcriptomic profiles of female and male P. chinensis flower buds. In total, 50,925,088 and 51,470,578 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 83,370 unigenes with a mean length of 1.3 kb were screened. Overall, 64,539 unigenes (77.48%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG, and GO databases, 71 of which were putatively related to the floral development of P. chinensis. Additionally, 21,662 simple sequence repeat (SSR) motifs were identified in 17,028 unigenes of P. chinensis, and the mononucleotide motif was the most dominant type of repeats (52.59%) in P. chinensis, followed by dinucleotide (22.29%), trinucleotide (20.15%). The most abundant repeats were AG/CT (13.97%), followed by AAC/GTT (6.75%) and AT/TA (6.10%). Based on these SSR, 983 EST-SSR primers were designed, 151 of which were randomly chosen for validation. Of these validated EST-SSR markers, 25 SSR markers were found to be polymorphic between male and female plants. One SSR marker, namelyPCSSR55, displayed excellent specificity in female plants, which could clearly distinguish between male and female P. chinensis. Altogether, our findings not only reveal that the EST-SSR marker is extremely effective in distinguishing between male and female P. chinensis but also provide a solid framework for sex determination of plant seedlings.

Fish-specific TLR18 in Nile tilapia (Oreochromis niloticus) recruits MyD88 and TRIF to induce expression of effectors in NF-κB and IFN pathways in melanomacrophages

Toll-like receptors (TLRs) are evolutionarily conserved proteins of pattern recognition receptors (PRRs) and play a crucial role in innate immune systems recognition of conserved pathogen-related molecular samples (PAMPs). We identified and characterized TLR18 from Nile tilapia (Oreochromis niloticus), OnTLR18, to elucidate its role in tissue expression patterns, modulation of gene expression after microbial challenge and TLR ligands, subcellular localization in fish and human cells, and the possible effectors TLR18 induces in a melanomacrophage-like cell line (tilapia head kidney (THK) cells). OnTLR18 expression was detected in all tissues examined, with the highest levels in the intestine and the lowest in the liver. OnTLR18 transcript was up-regulated in immune-related organs after bacterial and polyinosinic-polycytidylic acid (poly I:C) challenges and in the THK cells after lipopolysaccharide (LPS) stimulation. In transfected THK and human embryonic kidney (HEK) 293 cells, OnTLR18 localizes in the intracellular compartment. OnMyD88 and OnTRIF, but not OnTIRAP, were co-immunoprecipitated with OnTLR18, suggesting that the former two molecules are recruited by OnTLR18 as adaptors. The constitutively active form of OnTLR18 induced the production of pro-inflammatory cytokines, type I interferon (IFN), and antimicrobial peptides such as tumor necrosis factor α, interferon (IFN) d2.13, tilapia piscidin (TP)2, TP3, TP4, and hepcidin in THK cells. Our results suggest that OnTLR18 plays an important role in innate immunity through initiating nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and IFN signaling pathways via OnMyD88 and OnTRIF and induces the production of various effectors in melanomacrophages.

Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

BACKGROUND

Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development in T. ravennae.

RESULTS

During the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented in the GO enrichment analyses and tests for differential expression (FDR p-value < 0.05). The differential expression of floral integrators observed in the early phases of inflorescence development diminished prior to inflorescence determinacy regulation. Differential expression analysis did not identify many unique genes at mid-inflorescence development stages, though typical biological processes involved in plant growth and development expressed abundantly. The increase in inflorescence determinacy regulatory elements and putative homeotic floral development unigenes at mid-inflorescence development coincided with the expression of multiple meiosis annotations and multicellular organism developmental processes. Analysis of seed development identified multiple unigenes involved in oxidative-reductive processes.

CONCLUSION

Reproduction in grasses is a dynamic system involving the sequential coordination of complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development in T. ravennae. These results provide insights into the molecular regulation of reproductive development and provide a foundation for future investigations and analyses, including genome annotation, functional genomics characterization, gene family evolutionary studies, comparative genomics, and precision breeding.

Characterization of antiviral immune response induced by poly(I:C) in macrophages of farmed large yellow croaker (Larimichthys crocea)

Fish tend to rely more on their innate immunity to executing defense against viral infection by inducing antiviral gene production. However, the expression pattern and underlying mechanism of fish antiviral responses have yet to be fully defined. In the present study, an in vitro viral infection model was established by exposing head kidney-derived macrophages of large yellow croaker to virus analog, poly(I:C). Transcriptome analysis indicated that poly(I:C) appeared to induce potent antiviral activity featuring dominant interferon a3 (IFNa3) expression through activation of toll-like receptors (TLRs)/TIR-domain-containing adapter-inducing interferon-β (TRIF) and retinoic acid-inducible gene I-like receptors (RLRs)/mitochondrial antiviral signaling protein (MAVS) pathways. Inhibition of nuclear factor κB (NF-κB) and stimulator of interferon genes (STING)/interferon regulatory factor 3 (IRF3) pathways diminished the expression of IFNa3. Mechanistically, transcription factors including p65 and IRF3 could promote expression of IRF3, and activated IRF3 alone further increased the transcriptional activity of IFNa3. We also characterized the promoter of IFNa3 with direct IRF3 binding site which was sufficient to render the transcription of IFNa3. This effect was attenuated after deletion or mutation of the IRF3 binding sites. Taken together, our findings illustrate the distinct transcriptional profiling of fish macrophages triggered by poly(I:C). Also, this work provides new insights into the molecular mechanism underpinning coordinated activation of pathogen recognition and signaling transduction in the antiviral responses of non-model fish species.

Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus

Duck Tembusu virus (DTMUV), the causative agent of egg-drop syndrome, has caused substantial economic losses to duck industry. DTMUV infection leads to profound changes of host cells, including transcriptome and proteome. However, the lncRNA expression profile and the biological function of lncRNA have not been revealed. Therefore, DTMUV was used to inoculate duck embryo fibroblast cells (DEFs) for high-throughput RNA-sequencing (RNA-Seq). The results showed that 34 and 339 differently expressed lncRNAs were, respectively, identified at 12 and 24 h post-infection (hpi). To analyze their biological functions, target genes in cis were searched and the regulatory network was formed. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the target genes were strongly associated with immune system, signaling molecular and interaction, endocrine system, and signal transduction. The differently expressed lncRNAs were selected and verified by quantitative real-time polymerase chain reaction (RT-qPCR). Our study, for the first time, analyzed a comprehensive lncRNA expression profile in DEFs following DTMUV infection. The analysis provided a view on the important roles of lncRNAs in gene regulation and DTMUV infection.

Gill transcriptomes reveal expression changes of genes related with immune and ion transport under salinity stress in silvery pomfret (Pampus argenteus)

Salinity is a major ecological factor in the marine environment, and extremely important for the survival, development, and growth of fish. In this study, gill transcriptomes were examined by high-throughput sequencing at three different salinities (12 ppt as low salinity, 22 ppt as control salinity, and 32 ppt as high salinity) in an importantly economical fish silvery pomfret. A total of 187 genes were differentially expressed, including 111 up-regulated and 76 down-regulated transcripts in low-salinity treatment group and 107 genes differentially expressed, including 74 up-regulated and 33 down-regulated transcripts in high-salinity treatment group compared with the control group, respectively. Some pathways including NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction, Toll-like receptor pathway, cardiac muscle contraction, and vascular smooth muscle contraction were significantly enriched. qPCR analysis further confirmed that mRNA expression levels of immune (HSP90A, IL-1β, TNFα, TLR2, IP-10, MIG, CCL19, and IL-11) and ion transport-related genes (WNK2, NPY2R, CFTR, and SLC4A2) significantly changed under salinity stress. Low salinity stress caused more intensive expression changes of immune-related genes than high salinity. These results imply that salinity stress may affect immune function in addition to regulating osmotic pressure in silvery pomfret.

Advancing the fathead minnow (Pimephales promelas) as a model for immunotoxicity testing: Characterization of the renal transcriptome following Yersinia ruckeri infection

Recent studies have utilized the fathead minnow (Pimephales promelas) to explore the immunotoxic effects associated with a variety of environmental contaminants in the absence of immunological stimuli. Though this approach allows for alterations in the resting immune system to be detected, previous evidence suggests that many immunotoxic effects may only manifest in the activated immune system. However, basic immune responses to pathogens have not been well described in this species. To expand the utility of the fathead minnow as a model for immunotoxicity testing, a more comprehensive understanding of the activated immune system is required. As such, the main goal of this study was to characterize the transcriptomic response to pathogen infection in the fathead minnow using RNA sequencing. To achieve this goal, female fathead minnows were intraperitoneally injected with either Hank's Balanced Salt Solution (sham-injected) or Yersinia ruckeri (pathogen-injected). Eight hours following injection, fish were sacrificed for the assessment of general morphological (i.e., mass, length, condition factor, hepatic index) and immunological (i.e., leukocyte counts, spleen index) endpoints. To assess the molecular immune response to Y. ruckeri, kidney tissue was collected for transcriptomic analysis. A comparison of sham- and pathogen-injected fish revealed that >1800 genes and >500 gene networks were differentially expressed.Gene networks associated with inflammation, innate immunity, complement, hemorrhaging and iron absorption are highlighted and their utility within the context of immunotoxicity is discussed. These data reveal pathogen-related molecular endpoints to improve data interpretation of future studies utilizing the fathead minnow as a model for immunotoxicity.

Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon

BACKGROUND

Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising either from selective breeding (i.e. domestication) or genetic modification. Such distinct routes to accelerated growth may have unique implications for relationships and/or trade-offs between growth and immune function.

RESULTS

RNA-Seq was performed on liver and head kidney in four 'growth response groups' injected with polyinosinic-polycytidylic acid (Poly I:C; viral mimic), peptidoglycan (PGN; bacterial mimic) or PBS (control). These groups were: 1) 'W': wild-type, 2) 'TF': growth hormone (GH) transgenic salmon with ~ 3-fold higher growth-rate than W, 3) 'TR': GH transgenic fish ration restricted to possess a growth-rate equal to W, and 4) 'D': domesticated non-transgenic fish showing growth-rate intermediate to W and TF. D and TF showed a higher similarity in transcriptomic response compared to W and TR. Several immune genes showed constitutive expression differences among growth response groups, including perforin 1 and C-C motif chemokine 19-like. Among the affected immune pathways, most were up-regulated by Poly I:C and PGN. In response to PGN, the c-type lectin receptor signalling pathway responded uniquely in TF and TR. In response to stimulation with both immune mimics, TR responded more strongly than other groups. Further, group-specific pathway responses to PGN stimulation included NOD-like receptor signalling in W and platelet activation in TR. TF consistently showed the most attenuated immune response relative to W, and more DEGs were apparent in TR than TF and D relative to W, suggesting that a non-satiating ration coupled with elevated circulating GH levels may cause TR to possess enhanced immune capabilities. Alternatively, TF and D salmon are prevented from acquiring the same level of immune response as TR due to direction of energy to high overall somatic growth. Further study of the effects of ration restriction in growth-modified fishes is warranted.

CONCLUSIONS

These findings improve our understanding of the pleiotropic effects of growth modification on the immunological responses of fish, revealing unique immune pathway responses depending on the mechanism of growth acceleration and nutritional availability.

Genome-Wide Association Mapping and Gene Expression Analyses Reveal Genetic Mechanisms of Disease Resistance Variations in Cynoglossus semilaevis

The sustainable development of aquaculture has been impeded by infectious diseases worldwide. However, the genomic architecture and the genetic basis underlying the disease resistance remain poorly understood, which severely hampers both the understanding of the evolution of fish disease resistance traits and the prevention of these diseases in the aquaculture community. Cynoglossus semilaevis is a representative and commercially-important flatfish species. Here we combined genome-wide association study and Fst and nucleotide diversity filtration to identify loci important for the disease resistance. Based on 1,016,774 single-nucleotide polymorphisms (SNPs) identified from 650 Gb genome resequencing data of 505 individuals, we detected 33 SNPs significantly associated with disease resistance and 79 candidate regions after filtration steps. Both the allele frequencies and genotype frequencies of the associated loci were significantly different between the resistant and susceptible fish, suggesting a role in the genetic basis of disease resistance. The SNP with strongest association with disease resistance was located in Chr 17, at 145 bp upstream of fblx19 gene, and overlapped with the major quantitative trait locus previously identified. Several genes, such as plekha7, nucb2, and fgfr2, were also identified to potentially play roles in the disease resistance. Furthermore, the expression of some associating genes were likely under epigenetic regulations between the bacterial resistant and susceptible families. These results provide insights into the mechanism that enable variation of disease resistance to bacterial pathogen infection. The identified polymorphisms and genes are valuable targets and molecular resources for disease resistance and other traits, and for advanced breeding practice for superior germplasm in fish aquaculture.

Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink)

Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.

Gene Expression Profiles of Two Coral Species with Varied Resistance to Ocean Acidification

Recent studies have indicated that various corals might have different degrees of resistance to elevated CO₂ levels. However, the underlying molecular mechanism accounting for these differences is still poorly understood. In this study, RNA-seq data were analyzed to identify differentially expressed genes in two coral species (Acropora austera and Acropora cerealis) in response to high CO₂ levels. The calcification rates were higher in high CO₂ treatment than the control in A. austera, but was not significantly different in A. cerealis. A KEGG database search revealed that in both coral species, most Ca²⁺ transporters were present in the calcium signaling pathway, which could be important in the CO₂ regulation of coral calcification. The gene expression levels of many CO₂ and HCO₃^- transporters were not affected by elevated CO₂. Nevertheless, high CO₂ levels did have an effect on the expression of certain Ca²⁺ transporters. The upregulation of Ca²⁺ transporters likely explained the higher resistance of A. austera to high CO₂ than A. cerealis.

Global Transcriptomic Profiling of Pulmonary Gene Expression in an Experimental Murine Model of Rickettsia conorii Infection

Mediterranean spotted fever develops from an infection with Rickettsia conorii, an obligate intracellular, Gram-negative, endotheliotropic, and tick-transmitted bacterial pathogen, and is an acute, febrile illness that can progress to life-threatening complications if not diagnosed and treated early with effective antibiotics. Despite significant morbidity and mortality, little is known about changes in gene expression that determine the host responses during in vivo infection. We have investigated the transcriptional landscape of host lungs as a prominently affected organ system in an established murine model of infection by RNA-sequencing. Ingenuity pathway analysis resulted in the identification of 1332 differentially expressed genes and 292 upstream regulators. Notably, genes encoding for ubiquitin D, aconitate decarboxylase, antimicrobial peptides, calgranulins, cytokines and chemokines, and guanylate binding proteins were highly up-regulated, whereas those involved in hemoglobin biosynthesis and heme homeostasis were significantly down-regulated. Amongst response regulators, nucleotide-binding oligomerization domain-containing protein 2 and killer cell lectin-like receptors were differentially expressed, and gene clustering revealed eukaryotic initiation factor-2, oxidative phosphorylation, and ubiquitination as the predominantly activated biological pathways. Collectively, this first global transcriptomic profiling has identified R. conorii-induced regulation of novel genes and pathways in the host lungs, further in-depth investigation of which will strengthen our understanding of the pathogenesis of human rickettsioses.

De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids

BACKGROUND

Strongylocentrotus nudus is an important cultured sea urchin species in north China, because its gonad is rich in unsaturated fatty acids, particularly long polyunsaturated fatty acids (LC-PUFAs). These PUFAs play pleiotropic and crucial roles in a wide range of biological process.

OBJECTIVE

However, the genes contributing to biosynthesis PUFAs have not been elucidated yet, and the molecular mechanism relative to the difference in PUFA composition between male and female gonad as been revealed but the corresponding has not been understood.

METHODS

In this paper, solexa sequencing based transcriptomic approach was used to identify and characterize the key genes relative to PUFA synthesis and further conducted different expressed genes between male and female gonad.

RESULTS

A total of 130,124 transcripts and 189330 unigenes were de novo assembled from 64.32 Gb data. Next, these unigenes were subjected to functional annotation by mapping to six public databases, and this process revealed a lot of genes involving in lipid metabolism. In addition, three types of fatty acids front-end desaturase and three species of very long fatty acids elongase were identified and the pathway for PUFA biosynthesis was hypothesized. Last, comparative analysis revealed the higher expression level of Δ5 desaturase, Δ6 desaturase, ELOVL-4, -6 and -7 in male gonad compared with female.

CONCLUSION

This results could plausible explain the differ in composition of PUFAs between male and female gonad of sea urchin.

Analysis of the Gynaephora qinghaiensis pupae immune transcriptome in response to parasitization by Thektogaster sp

As a pest on the Qinghai-Tibet Plateau, Gynaephora qinghaiensis causes severe damage to grassland vegetation and its pupae are also natural hosts of Thektogaster sp. To successfully parasitize, endoparasitoids generally introduce or secrete multiple parasitic factors into the host body during the spawning stage to suppress the host immune response. To study the parasitic effects of Thektogaster sp. on G. qinghaiensis, a transcriptome analysis of immune-related genes in parasitized and nonparasitized G. qinghaiensis pupae was performed. A total of 371,260,704 clean reads were assembled into 118,144 unigenes with an average length of 884.33 base pairs. Of these, 23,660 unigenes were annotated in at least one database and 94,484 unigenes were not annotated in any databases. These findings indicated that the majority of the genetic resources (79.97% of all unigenes) in Gynaephora should be further explored. Parasitization significantly affected the transcriptional profile of G. qinghaiensis pupae. The present study identified 12,322 differentially expressed genes and 57 immune-related genes were identified in parasitized G. qinghaiensis pupae. Most immune-related genes were downregulated, potentially resulting from the inhibitory effect of Thektogaster sp. on G. qinghaiensis pupae after parasitization. Overall, the transcriptome analysis sheds valuable light on the molecular mechanisms of G. qinghaiensis parasitization by Thektogaster sp. and promotes the development of novel biocontrol strategies for Gynaephora based on immune defense.

Irf3 from mandarin fish thymus initiates interferon transcription

Interferon regulatory factors (IRFs) are transcription factors of the interferon (IFN)-inducible signaling pathway essential for host immunity against antimicrobial infection by virus and bacteria. Interferon regulatory factor 3 (IRF3) regulates the expression of IFNs and IFN-stimulated genes by binding to the IFN stimulatory response element (ISRE). In this study, we analyze the thymus transcriptome of the mandarin fish Siniperca chuatsi and report the functional analysis of Irf3 from the thymus as an emerging model of antiviral approaches. The predicted S. chuatsi IRF3 (Sc-Irf3) protein has 465 amino acid residues and evolutionarily conserved domains and is clustered in the IRF3 subfamily on a phylogenetic tree. Sc-Irf3 upon transgenic expression was mainly found in the cytoplasm through Western blot analysis and microscopy, but it translocated to the nucleus after polyinosinic:polycytidylic acid (ploly I:C) treatment. Endogenous Sc-irf3 RNA expression was detected in all eight adult organs examined. Importantly, Sc-irf3 RNA expression was significantly upregulated by ploly(I:C) treatment in the adult organs. Concurrently, reporter assays revealed that Sc-Irf3 increased the transcriptional activity of the ifnβ promoter, a minimal ISRE-containing promoter, and ifn promoter of mandarin fish. Therefore, Sc-Irf3 plays a major role in the IFN immune defense system against virus infection.

Transcriptome and Proteome Alternation With Resistance to Bacillus thuringiensis Cry1Ah Toxin in Ostrinia furnacalis

Background: Asian corn borer (ACB), Ostrinia furnacalis can develop resistance to transgenic Bacillus thuringiensis (Bt) maize expressing Cry1Ah-toxin. However, the mechanisms that regulate the resistance of ACB to Cry1Ah-toxin are unknown.

Objective: In order to understand the molecular basis of the Cry1Ah-toxin resistance in ACB, “omics” analyses were performed to examine the difference between Cry1Ah-resistant (ACB-AhR) and susceptible (ACB-BtS) strains of ACB at both transcriptional and translational levels.

Results: A total of 7,007 differentially expressed genes (DEGs) and 182 differentially expressed proteins (DEPs) were identified between ACB-AhR and ACB-BtS and 90 genes had simultaneous transcription and translation profiles. Down-regulated genes associated with Cry1Ah resistance included aminopeptidase N, ABCC3, DIMBOA-induced cytochrome P450, alkaline phosphatase, glutathione S-transferase, cadherin-like protein, and V-ATPase. Whereas, anti-stress genes, such as heat shock protein 70 and carboxylesterase were up-regulated in ACB-AhR, displaying that a higher proportion of genes/proteins related to resistance was down-regulated compared to up-regulated. The Kyoto encyclopedia of genes and genomes (KEGG) analysis mapped 578 and 29 DEGs and DEPs, to 27 and 10 pathways, respectively (P < 0.05). Furthermore, real-time quantitative (qRT-PCR) results based on relative expression levels of randomly selected genes confirmed the “omics” response.

Conclusion: Despite the previous studies, this is the first combination of a study using RNA-Seq and iTRAQ approaches on Cry1Ah-toxin binding, which led to the identification of longer length of unigenes in ACB. The DEGs and DEPs results are valuable for further clarifying Cry1Ah-mediated resistance.

An amino acid duplication/insertion in the Bm126 gene of Bombyx mori nucleopolyhedrovirus alters viral gene expression as shown by differential gene expression analysis

Open reading frame (ORF) 126 (Bm126) of Bombyx mori nucleopolyhedrovirus (BmNPV) is not essential for viral replication, and two subtypes of this gene have been identified in China. The Bm126-SX subtype encodes a protein with a simple amino acid duplication/insertion relative to the Bm126-GD subtype; however, significant differences in the cytopathic effect and infectivity of viruses carrying these variant genes have been observed. To elucidate the cause of these differences, differential gene expression analysis was performed at the early stage of infection with viruses harbouring variants of Bm126. Differential expression was observed for 103, 209, and 313 host genes and 9, 44, and 67 viral genes in vGD126 samples relative to the control samples (vSX126) at 6, 12, and 24 h postinfection, respectively. These results indicated that the duplication/insertion in Bm126 altered the viral expression pattern. The differentially expressed host genes were found to be related to ribosome, spliceosome, and proteasome pathways, and several factors involved in signal transduction were also identified. The differential expression of these viral and host genes was confirmed by qPCR. This study indicates that the amino acid duplication/insertion in the Bm126 gene has a biological function related to the regulation of viral gene expression and serves as a basis for further characterization of Bm126 gene function.

Transcriptomics analysis reveals candidate genes and pathways for susceptibility or resistance to Singapore grouper iridovirus in orange-spotted grouper (Epinephelus coioides)

In this study, the transcriptional response of grouper to Singapore grouper iridovirus (SGIV) stimulation was characterized using RNA sequencing. Transcriptome sequencing of three test groups in the grouper was performed using the Illumina MiSeq platform. The three test groups were a control group, which was injected with PBS buffer; a high-susceptible (HS) group, which died shortly after the SGIV injection; and a high-resistance (HR) group, which survived the SGIV injection. In total, 38,253 unigenes were generated. When the HS group was compared with the control group, 885 unigenes were upregulated and 487 unigenes were downregulated. When the HR and control groups were compared, 1114 unigenes were upregulated and 420 were downregulated, and when the HR and HS groups were compared, 1010 unigenes were upregulated and 375 were downregulated. In the KEGG analysis, two immune-related pathways, the p53 and peroxisome proliferator-activated receptor pathways, were detected with highly significant enrichment. In addition, 7465 microsatellites and 22,1569 candidate single nucleotide polymorphisms were identified from our transcriptome data. The results suggested several pathways that are associated with traits of disease susceptibility or disease resistance, and provided extensive information about novel gene sequences, gene expression profiles, and genetic markers. This may contribute to vaccine research and a breeding program against SGIV infection in grouper.

Transcriptome analysis of Aeromonas hydrophila infected hybrid sturgeon (Huso dauricus×Acipenser schrenckii)

The hybrid sturgeon (Huso dauricus × Acipenser schrenckii) is an economically important species in China. With the increasing aquaculture of hybrid sturgeon, the bacterial diseases are a great concern of the industry. In this study, de novo sequencing was used to compare the difference in transcriptome in spleen of the infected and mock infected sturgeon with Aeromonas hydrophila. Among 187,244 unigenes obtained, 87,887 unigenes were annotated and 1,147 unigenes were associated with immune responses genes. Comparative expression analysis indicated that 2,723 differently expressed genes between the infected and mock-infected group were identified, including 1,420 up-regulated and 1,303 down-regulated genes. 283 differently expressed anti-bacterial immune related genes were scrutinized, including 168 up-regulated and 115 down-regulated genes. Ten of the differently expressed genes were further validated by qRT-PCR. In this study, toll like receptors (TLRs) pathway, NF-kappa B pathway, class A scavenger receptor pathway, phagocytosis pathway, mannose receptor pathway and complement pathway were shown to be up-regulated in Aeromonas hydrophila infected hybrid sturgeon. Additionally, 65,040 potential SSRs and 2,133,505 candidate SNPs were identified from the hybrid sturgeon spleen transcriptome. This study could provide an insight of host immune genes associated with bacterial infection in hybrid sturgeon.

RNA-Seq-based transcriptome analysis of reproduction- and growth-related genes in Lateolabrax japonicus ovaries at four different ages

Lateolabrax japonicus is an abundant marine aquatic fish species that is commonly cultured in East Asia due to its high commercial value. In this study, RNA-Seq analysis of L. japonicus was carried out to identify reproduction- and growth-related genes expressed in L. japonicus ovaries at different ages using Illumina sequencing technology. In total, 334,388,688 high-quality reads were obtained in four libraries, i.e., 4-year-old ovaries (4th_Ovary), 3-year-old ovaries (3rd_Ovary), 2-year-old ovaries (2nd_Ovary), and 1-year-old ovaries (1st_Ovary). The reads were then de novo assembled into 101,860 unigenes with an average unigene length of 879 bp. In total, 30,142 unigenes (29.59%) were annotated in public databases, including Nr database (Nr), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Cluster of Orthologous Groups of proteins (COG), based on sequence similarity. Comparative analysis revealed that there were 35,749, 43,657, and 36,819 differentially expressed genes (DEGs) in three comparisons (4th_Ovary versus 3rd_Ovary, 4th_Ovary versus 2rd_Ovary, and 4th_Ovary versus 1st_Ovary, respectively). In total, 24,295 DEGs were different expressed in 4th_Ovary. Enrichment and pathway analyses of the DEGs were also carried out to excavate the candidate genes related to reproduction and growth, and 402 genes that potential involved in the regulation of reproduction and growth were identified, e.g., GnRHR (GnRH receptor), GHR 2 (growth hormone receptor 2), I_LGF1R (insulin-like growth factor 1 receptor), etc. Our findings expanded the genomic resources of L. japonicus and provided fundamental information for further studies.

RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Background

In the past years, our laboratory successfully generated transgenic rainbow trout bearing cecropin P1 transgene. These fish exhibited resistant characteristic to infection by Aeromonas salmonicida, Infectious Hematopoietic Necrosis Virus (IHNV) and Ceratomyxa shasta (a parasitic pathogen). Previously, treating rainbow trout macrophage cells (RTS-11) with cecropin B, pleurocidin and CF17, respectively, resulted in elevated expression of two pro-inflammatory genes, e.g. cyclooxygenase-2 (cox-2) and interleukin-1β (il-1β). In addition, a profiling of global gene expression by 44 k salmonid microarray analysis was conducted, and the results showed that immune relevant processes have been perturbed in cecopin P1 transgenic rainbow trout. Therefore, we hypothesized that cecropin P1 may not only eliminate pathogens directly, but also modulate the host immune systems, leading to increased resistance against pathogen infections. To confirm this hypothesis, we performed de novo mRNA deep sequencing (RNA-Seq) to analyze the transcriptomic expression profiles in three immune competent tissues of cecropin P1 transgenic rainbow trout.

Results

De novo sequencing of mRNA of the rainbow trout spleen, liver and kidney tissues were conducted by second-generation Illumina system, followed by Trinity assembly. Tissue specific unigenes were obtained, and annotated according to the Gene Ontology (GO) and the Nucleotide Basic Local Alignment Search Tool (BLAST). Over 2000 differentially expressed genes (DEGs) were determined by normalized ratio of Reads Per Kilobase of transcript per million mapped reads (RPKM) among the transgenic and non-transgenic fish in a tissue specific manner, and there were 82 DEGs in common among the three tissues. In addition, the enrichment analysis according to Gene Ontology Biological Process (GO:BP), and Kyoto Encyclopedia of Genes and Genomes (KEGG) based pathway analysis associated with innate/adaptive immunity of fish were also performed to illustrate the altered immune-related functions in each tissue.

Conclusions

According to the RNA-Seq data, the correlations between alteration of gene expression profiles and the functional perturbations of the host immune processes were revealed. In comparison with the results of cDNA microarray analysis conducted by Lo et al., the overall results supported our hypothesis that the gene product of cecropin P1 transgene may not only directly eliminate pathogens, but also modulate the host immune system. Results of this study present valuable genetic information for Oncorhynchus mykiss, and will benefit future studies on the immunology of this fish species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5141-8) contains supplementary material, which is available to authorized users.

Integrative Transcriptomic and microRNAomic Profiling Reveals Immune Mechanism for the Resilience to Soybean Meal Stress in Fish Gut and Liver

In aquafeeds, fish-meal has been commonly replaced with plant protein, which often causes enteritis. Currently, foodborne enteritis has few solutions in regards to prevention or cures. The recovery mechanism from enteritis in herbivorous fish may further help understand prevention or therapy. However, few reports could be found regarding the recovery or resilience to fish foodborne enteritis. In this study, grass carp was used as an animal model for soybean meal induced enteritis and it was found that the fish could adapt to the soybean meal at a moderate level of substitution. Resilience to soybean meal stress was found in the 40% soybean meal group for juvenile fish at growth performance, morphological and gene expression levels, after a 7-week feeding trial. Furthermore, the intestinal transcriptomic data, including transcriptome and miRNAome, was applied to demonstrate resilience mechanisms. The result of this study revealed that in juvenile grass carp after a 7-week feeding cycle with 40% soybean meal, the intestine recovered via enhancing both an immune tolerance and wound healing, the liver gradually adapted via re-balancing immune responses, such as phagosome and complement cascades. Also, many immune factors in the gut and liver were systemically revealed among stages of on-setting, remising, and recovering (or relief). In addition, miRNA regulation played a key role in switching immune states. Thus, the present data systemically demonstrated that the molecular adaptation mechanism of fish gut-liver immunity is involved in the resilience to soybean meal stress.

Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals

The innate immune system is the first line of defense against pathogens, which is initiated by the recognition of pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs). Among all the PRRs identified, the toll-like receptors (TLRs) are the most ancient class, with the most extensive spectrum of pathogen recognition. Since the first discovery of Toll in Drosophila melanogaster, numerous TLRs have been identified across a wide range of invertebrate and vertebrate species. It seems that TLRs, the signaling pathways that they initiate, or related adaptor proteins are essentially conserved in a wide variety of organisms, from Porifera to mammals. Molecular structure analysis indicates that most TLR homologs share similar domain patterns and that some vital participants of TLR signaling co-evolved with TLRs themselves. However, functional specification and emergence of new signaling pathways, as well as adaptors, did occur during evolution. In addition, ambiguities and gaps in knowledge still exist regarding the TLR network, especially in lower organisms. Hence, a systematic review from the comparative angle regarding this tremendous signaling system and the scenario of evolutionary pattern across Animalia is needed. In the current review, we present overview and possible evolutionary patterns of TLRs in non-mammals, hoping that this will provide clues for further investigations in this field.

Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG

Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter found in the central nervous system of mammals. A range of bacterial species can synthesize GABA, including Lactobacillus plantarum of which L-monosodium glutamate (L-MSG) is an inducer of its production. In order to synthesize GABA in high concentrations, L-MSG was utilized as the single inducing factor, a chemically defined medium (CDM) was used as the fermentation substrate, with L. plantarum CGMCC 1.2437^T cultured in medium supplemented with or without L-MSG. High-throughput transcriptome sequencing was used to explore the differential genes expression of bacterial cells at 36 h of fermentation, where the GABA concentration of CDM with L-MSG reached the peak value and was 7.7 times higher than that of medium without L-MSG at the same timepoint. A total of 87 genes showed significant differential expression induced by L-MSG: of these, 69 were up-regulated genes and 18 were down-regulated. The up-regulated genes were assigned to biological processes and molecular function, while the down-regulated genes covered biological process, cellular process and molecular function. Interrogation of results using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, indicated carbohydrate metabolism, fatty acid synthesis and amino acid metabolism were closely associated with GABA synthesis induced by L-MSG. This study provides insights into L. plantarum-mediated GABA fermentation at the molecular level and will provide a new approach for further studies related to GABA production by the other Lactic acid bacteria.

Molecular mechanisms of an antimicrobial peptide piscidin (Lc-pis) in a parasitic protozoan, Cryptocaryon irritans

Background

Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling this parasite with chemicals or antibiotics are widely considered to be environmentally harmful. Piscidins with broad spectrum antibacterial, antifungal and antiviral activities were found to have potent activity against C. irritans. Little, however, has been understood about the killing mechanisms of piscidins in parasites.

Results

In total, 57.12, 50.44, 55.86 and 47.87 million raw reads were generated from untreated theront and trophont, and piscidin (Lc-pis) treated theront and trophont libraries, respectively. After de novo assembly, 966,609 unigenes were generated with an average length of 420 bp: among these, 618,629 unigenes showed identity with sequences in one or more databases, with some showing to be significantly manipulated by Lc-pis treatment. The species classification showed that more than 25.8% unigenes from trophonts were homologous to the large yellow croaker (Larimichthys crocea) and less than 3.8% unigenes from theronts were matched. The homologous unigenes demonstrated that the tissue from host could exist in trophonts and might be transported to parasite via vesicular transports. Our analysis showed that regulatory transcripts were involved in vesicular trafficking. Among transcripts induced by Lc-pis, most genes up-regulated in treated and untreated theronts were involved in cell migration and apoptosis related pathways. Few transcripts were found to be down-regulated in treated and untreated trophonts related to cell structure and migration after treatment.

Conclusions

This is the first transcriptome analysis of C. irritans exposed to Lc-pis, which enhanced the genomic resources and provided novel insights into molecular mechanisms of ciliates treated by cationic antimicrobial peptide. Our comprehensive transcriptome analysis can facilitate the identification of potential drug targets and vaccines candidates for controlling this devastating fish pathogen.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4565-5) contains supplementary material, which is available to authorized users.

Elevated CO2 delays the early development of scleractinian coral Acropora gemmifera

The effects of elevated CO₂ on the early life stages of coral were investigated by culturing the pelagic larvae and new recruits of Acropora gemmifera at three concentrations of CO₂ (corresponding to pH = 8.1, 7.8 and 7.5, respectively). Acidified seawater resulted in fewer A. gemmifera larvae settling, and led to the production of smaller new recruits by slowing the development of the skeleton. The delayed development of new recruits due to elevated CO₂ was consistent with the downregulation of calcification related genes. Several genes related to HCO₃^- and Ca²⁺ transporters were downregulated by elevated CO₂, with solute carriers (SLC) (membrane transport proteins) possibly playing an important role. The downregulation of these membrane transport proteins might suppress the transport of calcium, bicarbonate and organic matter, resulting in the delayed development of A. gemmifera.

Transcriptome analysis provides insights into the immune responsive pathways and genes in the head kidney of tiger grouper (Epinephelus fuscoguttatus) fed with Spatholobus suberectus, Phellodendron amurense, or Eclipta prostrata

The tiger grouper, Epinephelus fuscoguttatus, is an economically important fish in Southeast Asia but has been plagued by several diseases. Spatholobus suberectus (S), Phellodendron amurense (P), and Eclipta prostrate (E) are three commonly used Chinese medicinal herbs. Although previous pharmacological and clinical studies indicated that S, P, and E possess a variety of beneficial functions in mammals, little is known about their functions in farmed fish and the underlying molecular mechanism of their actions. Challenge tests in this study showed that after 14 days of diet supplement, all these herbs could effectively enhance the disease resistance of E. fuscoguttatus against Vibrio harveyi. However, the non-specific immune parameters of the herb-supplemented groups were not significantly different from the control group. To further explore the molecular mechanism of herbal immune-regulating effects on E. fuscoguttatus, transcriptome sequencing and RNA-Seq technique were applied on E. fuscoguttatus kidney. De novo transcriptome assembly of E. fuscoguttatus kidney yield 80,014 unigenes, among which, 44,901 (56.12%) were annotated with at least one of the public databases (Nr, Nt, Swiss-Prot, KEGG, COG, GO). Among these, 22,738, 11,700 and 27,457 unigenes were assigned to 57, 25 and 258 categories of GO, COG and KEGG databases, respectively. Using Solexa/Illumina's DGE platform, a total of 231, 186 and 144 putative differentially expressed genes (DEGs) were detected in P, E and S group compared with the control group. GO analysis indicated that in P and E, down-regulated DEGs were dominant in almost every GO term; whereas in S, up-regulated DEGs were more dominant. KEGG pathway analysis revealed that putative DEGs in all three herb groups were obviously enriched in the pathways related to infective diseases and immune system. We also identified a number of immune relative genes and pathways (TLR5, IL8 and MAPK pathway, for instance) associated with P, E and S's regulatory effects on E. fuscoguttatus. This study will enrich the E. fuscoguttatus transcriptome database, contribute to a better understanding of the molecular mechanisms associated with the immunoregulatory activities of Chinese medicinal herbs on teleost and provide valuable information on the prevention of grouper Vibrio diseases using Chinese medicinal herbs.

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.

Non-mammalian Toll-like receptor 18 (Tlr18) recognizes bacterial pathogens in common carp (Cyprinus carpio L.): Indications for a role of participation in the NF-κB signaling pathway

Toll-like receptors are important pattern recognition receptors that can recognize pathogen-associated molecular patterns (PAMPs) and play a critical role in innate immunity. In the present study, tlr18 was identified from common carp (Cyprinus carpio L.) (named Cctlr18). The deduced amino acid sequence contained only a signal peptide, eight LRR (leucine-rich repeat) motifs, a transmembrane region and a TIR (Toll/IL-1 receptor) domain. Phylogenetic analysis showed that CcTlr18 was most closely related to Ctenopharyngodon idella Tlr18. Quantitative real-time PCR analysis showed that Cctlr18 was constitutively expressed in all investigated tissues with the highest expression level in the skin and lowest expression in the gonad. After injection with inactivated Aeromonas hydrophila, Cctlr18 expression was significantly up-regulated in the head kidney, foregut, hindgut and skin. Moreover, significant up-regulation of Cctlr8 was observed in the spleen, head kidney, hindgut and skin after immersion with live A. hydrophila. In addition, the expression of Cctlr18 was up-regulated in PGN or flagellin-stimulated HKLs. Luciferase reporter assays showed that Cctlr18 activated NF-κB in 293 T cells and that NF-κB activity was enhanced in Cctlr18 and Ccmyd88 co-transfected cells. Furthermore, Cctlr18 could induce the expression of cytokines genes, including ifn, il-1β and il-10, in EPC cells. The results suggested that Cctlr18 plays an important role in the immune response and provides basic information for investigating the mechanisms of fish tlr18.

Transcriptome profiling provides gene resources for understanding gill immune responses in Japanese flounder (Paralichthys olivaceus) challenged with Edwardsiella tarda

Marine organisms are commonly under threats from various pathogens. Edwardsiella tarda is one of the fish pathogens that seriously infect cultured and wild fish species. Bacteremia caused by E. tarda can be a fatal disease in humans. Fish gill is a mucosa-associated lymphoid tissue that directly contacted with sea water. Generating gill transcriptomic resources that challenged by E. tarda is crucial for understanding the molecular mechanisms underlying gill immune responses. In this study, we performed transcriptome profiling of gene expression in Japanese flounder gills (Paralichthys olivaceus) challenged by E. tarda with different stress duration. An average of 40 million clean reads per library were obtained, of which approximately 83.2% were successfully mapped to the reference genome. 456 and 1037 differential expressed genes (DEGs) were identified at 8 h and 48 h post-injection, respectively. Gene annotation analysis and protein-protein interaction networks were conducted to obtain the key interaction relationships of immune-related DEGs during pathogens infection. 24 hub genes with multiple protein-protein interaction relationships or involved in multiple KEGG signaling pathways were discovered and validated by qRT-PCR. These hub genes mainly participated in Leukocyte transendothelial migration signaling pathway, B cell receptor signaling pathway, Wnt signaling pathway and Apoptosis signaling pathway. This study represents the first gill transcriptomic analysis based on protein-protein interaction networks in fish and provides valuable gene resources for understanding the fish gill immunity, which can pave the way to understand the molecular mechanisms of immune responses with E. tarda infection.

Transcriptome profiling based on protein-protein interaction networks provides a core set of genes for understanding blood immune response mechanisms against Edwardsiella tarda infection in Japanese flounder (Paralichthys olivaceus)

Marine organisms are commonly under threat from various pathogens. Edwardsiella tarda is one of the fish pathogens that can infect both cultured and wild fish species. E. tarda can also infect other vertebrates, including amphibians, reptiles, and mammals. Bacteremia caused by E. tarda can be a fatal disease in humans. Blood acts as a pipeline for the fish immune system. Generating blood transcriptomic resources from fish challenged by E. tarda is crucial for understanding molecular mechanisms underlying blood immune response process. In this study, we performed transcriptome-wide gene expression profiling of Japanese flounder (Paralichthys olivaceus) challenged by 8 and 48 h E. tarda stress. An average of 37 million clean reads per library was obtained, and approximately 85.6% of these reads were successfully mapped to the reference genome. In addition, 808 and 1265 differential expression genes (DEGs) were found at 8 and 48 h post-injection, respectively. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to search immune-related DEGs. A protein-protein interaction network was constructed to obtain the interaction relationship of immune genes during pathogens stress. Based on KEGG and protein association networks analysis, 30 hub genes were discovered and validated by quantitative RT-PCR. This study represents the first transcriptome analysis based on protein-protein interaction networks in fish and provides us with valuable gene resources for the research of fish blood immunity, which can significantly assist us to further understand the molecular mechanisms of humans and other vertebrates against E. tarda.

Combined cytotoxicity of aflatoxin B1 and deoxynivalenol to hepatoma HepG2/C3A cells

Co-occurrence of aflatoxin B1 (AFB1) and deoxynivalenol (DON) is one of the most common mycotoxin contaminations in cereal crops and food ingredients. However, the mechanism of their combined toxicity is poorly understood. In the current investigation, the hepatoma HepG2/C3A cell line was used to explore the combined cytotoxicity of AFB1 and DON. The values of IC50, based on a sulforhodamine B (SRB) assay, were 4.5 mM and 18.7 mM for DON and AFB1, respectively. The analysis of cytotoxicity endpoints using the combination index (CI) theory revealed that the changes of mitochondrial membrane permeability and ATP resulted from an additive cytotoxic effect (CI≈1) of AFB1 and DON. However, the endpoints of double strand DNA (ds-DNA), reactive oxygen species (ROS) and cell viability (SRB) were synergistically (CI<1) affected in a dose-dependent manner. RNA-seq analysis demonstrated a number of uniquely expressed genes in their combination (AFB1: 2.5 mM, DON: 0.56 mM), indicating a synergistic interaction between AFB1 and DON at a molecular level. Additional transcriptomics analysis showed that the endoplasmic reticulum stress-associated JNK/p38/MAPK pathway was induced by DON, whereas the p53 signalling pathway was activated by AFB1. The expression profiles of apoptosis-related genes caspase-3, Bax and Bcl-2 suggested a mitochondria-mediated apoptosis pathway that was shared between AFB1 and DON. Thus, different cytotoxicity pathways and their converging at the apoptotic process might be the mechanism of the additive/synergistic cytotoxicity of AFB1 and DON to HepG2/C3A cells.

Toxic Effects and Molecular Mechanism of Different Types of Silver Nanoparticles to the Aquatic Crustacean Daphnia magna

Silver nanoparticles (AgNPs) have been assessed to have a high exposure risk for humans and aquatic organisms. Toxicity varies considerably between different types of AgNPs. This study aimed to investigate the toxic effects of AgNPs with different particle sizes (40 and 110 nm) and different surface coatings (sodium citrate and polyvinylpyrrolidone, PVP) on Daphnia magna and their mechanisms of action. The results revealed that the citrate-coated AgNPs were more toxic than PVP-coated AgNPs and that the 40 nm AgNPs were more toxic than the 110 nm AgNPs. Transcriptome analysis further revealed that the toxic effects of AgNPs on D. magna were related to the mechanisms of ion binding and several metabolic pathways, such as the "RNA polymerase" pathway and the "protein digestion and absorption" pathway. Moreover, the principal component analysis (PAC) results found that surface coating was the major factor that determines the toxicities compared to particle size. These results could help us better understand the possible mechanism of AgNP toxicity in aquatic invertebrates at the transcriptome level and establish an important foundation for revealing the broad impacts of nanoparticles on aquatic environments.

Temporal changes in innate immunity parameters, epinecidin gene expression, and mortality in orange-spotted grouper, Epinephelus coioides experimentally infected with a fish pathogen, Vibrio harveyi JML1

Changes in innate immunity parameters and epinecidin mRNA transcript levels were examined to characterize the non-specific immune response of E. coioides to pathogenic V. harveyi JML1 isolated from affected cage-cultured fish. After fish had been injected with bacteria at a dose causing 30% mortality, blood and tissue samples were collected at 0, 6, 12, 24, 48, 72, 96, 120, and 240 h post-infection (hpi) for assessment of indices such as the oxidative burst (OB) and phagocytic index (PI) of head kidney cells, and lysozyme activity (LYS) and total immunoglobulin (Total Ig) levels of the plasma. The epinecidin mRNA transcript levels (EGE) from skin, gills, liver, kidney, and spleen tissues were also determined by gel-based RT-PCR. Lastly, daily mortality (DM), liver total bacterial load (TBC), and presumptive Vibrio count (TVC) were monitored up to 240 hpi. The results revealed that bacteria proliferated rapidly in fish tissue, reaching peak densities at 24 hpi for both TBC and TVC but was on a downward trend thereafter. The pattern in fish mortality closely correlated with TBC and TVC. Total Ig, OB, and PI in E. coioides were suppressed in the early part of infection when V. harveyi load was high but recovered and later increased as bacterial density declined. LYS and EGE were consistently high and their activities were not hampered by bacterial infection. The study demonstrated that V. harveyi JML1 interacts with E. coioides by transiently inhibiting some immune parameters resulting in mortalities. However, consistently high LYS, upregulated EGE, and resurgent PI, OB and Total Ig conferred resistance and subsequent recovery in the fish. The study provides new insights on the interaction between E. coioides and V. harveyi JML1 that can aid in formulating health management strategies for groupers. Further studies on prophylactic interventions to enhance the innate immune response in grouper during infection with V. harveyi JML1 are suggested.

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

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

Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine

Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers.

Sequencing-based network analysis provides a core set of gene resource for understanding kidney immune response against Edwardsiella tarda infection in Japanese flounder

Marine organisms are under a frequent threat from various pathogens. Edwardsiella tarda is one of the major fish pathogens infecting both cultured and wild fish species. It can also infect a variety of other vertebrates, including amphibians, reptiles, and mammals, and bacteremia caused by E. tarda can be fatal in humans. The kidney is the largest lymphoid organ in fish, and generating kidney transcriptomic information under different stresses is crucial for understanding molecular mechanisms underlying the immune responses in the kidneys. In this study, we performed transcriptome-wide gene expression profiling of the Japanese flounder (Paralichthys olivaceus) challenged by 8 and 48 h of E. tarda infection. An average of 40 million clean reads per library was obtained, and approximately 81.6% of these reads were successfully mapped to the reference genome. In addition, 1319 and 4439 differentially expressed genes (DEGs) were found at 8 and 48 h post-injection, respectively. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to search immune-related DEGs. A protein-protein interaction network was constructed to ascertain the relationship between interacting immune genes during pathogen-induced stress. Based on the KEGG and protein association networks analysis, 24 hub genes were discovered and validated by qRT-PCR. To our knowledge, this study is the first to represent the kidney transcriptome analysis based on protein-protein interaction networks in fish. Our results provide valuable gene resources for further research on kidney immune response in fish, which can significantly improve our understanding of the molecular mechanisms underlying the immune response to E. tarda in humans and other vertebrates.

Correlation between RNA-Seq and microarrays results using TCGA data

RNA sequencing (RNA-Seq) and microarray are two of the most commonly used high-throughput technologies for transcriptome profiling; however, they both have their own inherent strengths and limitations. This research aims to analyze the correlation between microarrays and RNA-Seq detection of transcripts in the same tissue sample to explore the reproducibility between the techniques. Using data of RNA-Seq v2 and three different microarrays provided by The Cancer Genome Atlas, 11,120 genes of 111 lung squamous cell carcinoma samples were simultaneously detected by the four methods. Then we analyzed the Pearson correlation between microarrays and RNA-Seq. Finally, in the six comparison results, 9984 (89.8%) genes, irrespective of which two methods were used, simultaneously showed the existence of correlation, whereas only 83 (0.1%) genes proved to have no significant correlation in either comparison. In addition, the comparisons between 3266 (29.3%) genes showed high correlation (R≥0.8) in all six comparisons, only for 1643 (14.8%) genes correlation were not as high in either comparison. Meanwhile, transcripts with extreme high or low expression levels were more highly discrepant across the methods. In conclusion, we found that, for most transcripts, the results obtained by RNA-Seq and microarrays were highly reproducible.

Transcriptome differences between enrofloxacin-resistant and enrofloxacin-susceptible strains of Aeromonas hydrophila

Enrofloxacin is the most commonly used antibiotic to control diseases in aquatic animals caused by A. hydrophila. This study conducted de novo transcriptome sequencing and compared the global transcriptomes of enrofloxacin-resistant and enrofloxacin-susceptible strains. We got a total of 4,714 unigenes were assembled. Of these, 4,122 were annotated. A total of 3,280 unigenes were assigned to GO, 3,388 unigenes were classified into Cluster of Orthologous Groups of proteins (COG) using BLAST and BLAST2GO software, and 2,568 were mapped onto pathways using the Kyoto Encyclopedia of Gene and Genomes Pathway database. Furthermore, 218 unigenes were deemed to be DEGs. After enrofloxacin treatment, 135 genes were upregulated and 83 genes were downregulated. The GO terms biological process (126 genes) and metabolic process (136 genes) were the most enriched, and the terms for protein folding, response to stress, and SOS response were also significantly enriched.

This study identified enrofloxacin treatment affects multiple biological functions of A. hydrophila. Enrofloxacin resistance in A. hydrophila is closely related to the reduction of intracellular drug accumulation caused by ABC transporters and increased expression of topoisomerase IV.

Transcriptome profiling and digital gene expression analysis of the skin of Dybowski's frog (Rana dybowskii) exposed to Aeromonas hydrophila

Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A. hydrophila. In this work, a total of 26,244,446 transcriptome sequencing reads were obtained and assembled into 109,089 unique unigenes using de novo assembly, and a total of 37,105 unigenes (34.0%) were functionally annotated against the non-redundant (Nr), Swiss-Prot, Cluster of Orthologous Groups of Proteins (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Gene expression changes in the skin tissue of R. dybowskii exposed to A. hydrophila were investigated by a tag-based DGE system, and a total of 1435 significantly differentially expressed genes were identified, including 460 that were up-regulated and 975 that were down-regulated, indicating a large change in the host transcriptome profile exposed to A. hydrophila. Among these, 478 genes were associated with immune-relevant pathways, metabolic pathways, cellular components, growth, migration, and muscle and hormone signaling pathways. We confirmed the differential expression of 106 immune-relevant genes associated with innate and adaptive immune responses. Our data provide a fairly comprehensive molecular biology background for the deeper understanding of the amphibian immune system following A. hydrophila infection.

Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection

Grouper is one of the favorite sea food resources in Southeast Asia. However, the outbreaks of the viral nervous necrosis (VNN) disease due to nervous necrosis virus (NNV) infection have caused mass mortality of grouper larvae. Many aqua-farms have suffered substantial financial loss due to the occurrence of VNN. To better understand the infection mechanism of NNV, we performed the transcriptome analysis of sevenband grouper brain tissue, the main target of NNV infection. After artificial NNV challenge, transcriptome of brain tissues of sevenband grouper was subjected to next generation sequencing (NGS) using an Illumina Hi-seq 2500 system. Both mRNAs from pooled samples of mock and NNV-infected sevenband grouper brains were sequenced. Clean reads of mock and NNV-infected samples were de novo assembled and obtained 104,348 unigenes. In addition, 628 differentially expressed genes (DEGs) in response to NNV infection were identified. This result could provide critical information not only for the identification of genes involved in NNV infection, but for the understanding of the response of sevenband groupers to NNV infection.