De novo whole transcriptome analysis of the fish louse, Argulus siamensis: first molecular insights into characterization of Toll downstream signalling molecules of crustaceans

Transcriptomic analysis revealed the dynamic response mechanism to acute ammonia exposure in the ivory shell, Babylonia areolata

The ivory shell (Babylonia areolata) is an economically important shellfish in tropical and subtropical regions, but its intensive culture and biological characteristic of hiding in the sandy substrate make it highly susceptible to ammonia stress. In this study, we investigated the dynamic changes in histopathology, oxidative stress, and transcriptome of the ivory shell at different time points under high concentration (60 mg/L) ammonia exposure. With prolonged exposure to stress, vacuoles appeared in the hepatopancreas while cell volume and intercellular space increased. The activities of superoxide dismutase (SOD) and catalase (CAT) decreased significantly under high concentrations of ammonia-induced stress while malondialdehyde (MDA) levels increased significantly. Integrated analysis of differentially expressed genes (DEGs), weighted gene co-expression network analysis (WGCNA), and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that lipid transport primarily contributed to maintaining cellular homeostasis during the early stage of stress (6 and 12 h). Subsequently, a significant upregulation of oxidation-reduction reactions occurred at the middle stage (24 h), leading to oxidative stress. Finally, during the later stage (48 h), metabolic decomposition provided energy for survival maintenance. Additionally, lysosome and apoptosis were identified as potential key pathways in response to acute ammonia toxicity. Overall, our findings suggest that ivory shells can respond to acute ammonia toxicity via immune and antioxidant defense mechanisms but sustained high concentrations may cause irreversible damage. This study provides valuable insights into the response mechanism of mollusks towards ammonia and serves as a data reference for breeding ammonia-tolerant varieties of ivory shells.

An insight into the interaction between Argulus siamensis and Labeo rohita offers future therapeutic strategy to combat argulosis

Aquaculture and fisheries are salient flourishing sectors in the world but their sustainability is often afflicted by several pathogenic diseases. Among all the pathogenic diseases of fish, parasitic diseases are found to be a major cause of concern. Argulosis is one of the dominant parasitic problems encountered in Indian aquaculture practices. Argulus siamensis is the most prevalent argulid species harming the Indian major carp species including Labeo rohita. The major carps respond to parasitic infestation by elevating various immune relevant genes. The therapeutic chemicals, synthetic drugs and other plant extracts have made a progress in the fight against argulosis. However, there is no effective vaccine and drugs are available for this disease. Thus, designing efficient, cost-effective and eco-friendly control and treatment strategies for argulosis is presently needed. Keeping the aforementioned facts in mind, the current review elaborated the immunological interaction between A. siamensis and L. rohita, available combat tactics, highlighted the already identified vaccine candidates to design effective control measures and illustrated the use of omics technology in future to combat argulosis.

Daily patterns in parasite processes: diel variation in fish louse transcriptomes

Parasites, similar to all other organisms, time themselves to environmental cues using a molecular clock to generate and maintain rhythms. Chronotherapeutic (timed treatment) techniques based on such rhythms offer great potential for improving control of chronic, problematic parasites. Fish lice are a key disease threat in aquaculture, with current control insufficient. Assessing the rhythmicity of fish lice transcriptomes offers not only insight into the viability of chronotherapy, but the opportunity to identify new drug targets. Here, for the first known time in any crustacean parasite, diel changes in gene transcription are examined, revealing that approximately half of the Argulus foliaceus annotated transcriptome displays significant daily rhythmicity. We identified rhythmically transcribed putative clock genes including core clock/cycle and period/timeless pairs, alongside rhythms in feeding-associated genes and processes involving immune response, as well as fish louse drug targets. A substantial number of gene pathways showed peak transcription in hours immediately preceding onset of light, potentially in anticipation of peak host anti-parasite responses or in preparation for increased feeding activity. Genes related to immune haemocyte activity and chitin development were more highly transcribed 4 h post light onset, although inflammatory gene transcription was highest during dark periods. Our study provides an important resource for application of chronotherapy in fish lice; timed application could increase efficacy and/or reduce dose requirement, improving the current landscape of drug resistance and fish health while reducing the economic cost of infection.

The immune response of fairy shrimp Streptocephalus sirindhornae against bacterial black disease by de novo transcriptome analysis

To enhance genomic resources and to understand the molecular immune mechanisms underlying the response of fairy shrimp (Streptocephalus sirindhornae) to pathogens, we first performed a comparative gene transcription analysis from Aeromonas hydrophila-immunized shrimp and from a control group through RNA sequencing. Meanwhile, the differentially expressed genes (DEGs) were investigated, and a total of 46,958,894 clean reads were obtained and then assembled into 73,297 unigenes with an average length of 993 bp and an N50 of 1,458 bp. Unigenes were annotated by comparison with the NR/NT/KO/SwissProt/PFAM/GO and KOG databases, and 28,198 unigenes (38.47%) were annotated in at least one database. After a bacterial challenge, 143 and 287 genes were identified as markedly up- or downregulated, respectively, and 345 were associated with 142 pathways, including the classic immune-related apoptosis, toll-like receptor and MAPK signaling pathways. Moreover, ten differently expressed immune-related genes were confirmed by using quantitative real-time PCR. This study characterized a gene expression pattern for normal and Aeromonas hydrophila-immunized S. sirindhornae for the first time and shed new light on its molecular mechanisms, thus enabling the future efforts of disease control programs for this valuable aquaculture species.

Development of Fish Parasite Vaccines in the OMICs Era: Progress and Opportunities

Globally, parasites are increasingly being recognized as catastrophic agents in both aquaculture sector and in the wild aquatic habitats leading to an estimated annual loss between 1.05 billion and 9.58 billion USD. The currently available therapeutic and control measures are accompanied by many limitations. Hence, vaccines are recommended as the "only green and effective solution" to address these concerns and protect fish from pathogens. However, vaccine development warrants a better understanding of host-parasite interaction and parasite biology. Currently, only one commercial parasite vaccine is available against the ectoparasite sea lice. Additionally, only a few trials have reported potential vaccine candidates against endoparasites. Transcriptome, genome, and proteomic data at present are available only for a limited number of aquatic parasites. Omics-based interventions can be significant in the identification of suitable vaccine candidates, finally leading to the development of multivalent vaccines for significant protection against parasitic infections in fish. The present review highlights the progress in the immunobiology of pathogenic parasites and the prospects of vaccine development. Finally, an approach for developing a multivalent vaccine for parasitic diseases is presented. Data sources to prepare this review included Pubmed, google scholar, official reports, and websites.

Selection of candidate reference genes for RT-qPCR analysis in Argulus siamensis and their validation through screening of drugs and drug targets

Argulus spp. are economically important fish ectoparasites. The development of antiparasitic drugs is thus important and real time PCR is an indispensable tool in drug development. The analytical potential of RT-PCR depends upon accurate normalisation by the use of stable reference genes. Here, we identified stable reference genes of Argulus siamensis for validation of efficacy of drugs and drug targets. Seven candidate genes were evaluated by evaluating their expression under different states of Argulus using the RefFinder tool. The four algorithms together generated a comprehensive ranking with elongation factor-1 alpha (EF-1α) being the most stable and 18S ribosomal protein (18S) the least stable gene. Taking EF-1α and 18S genes as references, the effectiveness of six anti-parasitic compounds against Argulus was evaluated by studying their effect on the expression pattern of few ion channel genes; this was to understand their mode of action, besides validating the reference genes. EF-1α was found to be the most stable gene in the validation. Collectively, this study is the first report to validate the optimal reference genes of A. siamensis for normalisation, and the potential of the ion channel genes for evaluating effective drug targets in parasite control.

Evolutionary emergence of Hairless as a novel component of the Notch signaling pathway

Suppressor of Hairless [Su(H)], the transcription factor at the end of the Notch pathway in Drosophila, utilizes the Hairless protein to recruit two co-repressors, Groucho (Gro) and C-terminal Binding Protein (CtBP), indirectly. Hairless is present only in the Pancrustacea, raising the question of how Su(H) in other protostomes gains repressive function. We show that Su(H) from a wide array of arthropods, molluscs, and annelids includes motifs that directly bind Gro and CtBP; thus, direct co-repressor recruitment is ancestral in the protostomes. How did Hairless come to replace this ancestral paradigm? Our discovery of a protein (S-CAP) in Myriapods and Chelicerates that contains a motif similar to the Su(H)-binding domain in Hairless has revealed a likely evolutionary connection between Hairless and Metastasis-associated (MTA) protein, a component of the NuRD complex. Sequence comparison and widely conserved microsynteny suggest that S-CAP and Hairless arose from a tandem duplication of an ancestral MTA gene.

Neuropeptide discovery in Proasellus cavaticus: Prediction of the first large-scale peptidome for a member of the Isopoda using a publicly accessible transcriptome

In silico transcriptome mining is one of the most effective methods for neuropeptide discovery in crustaceans, particularly for species that are small, rare or from geographically inaccessible habitats that make obtaining the large pools of tissue needed for other peptide discovery platforms impractical. Via this approach, large peptidomes have recently been described for members of many of the higher crustacean taxa, one notable exception being the Isopoda; no peptidome has been predicted for any member of this malacostracan order. Using a publicly accessible transcriptome for the isopod Proasellus cavaticus, a subcentimeter subterranean ground water dweller, the first in silico-predicted peptidome for a member of the Isopoda is presented here. BLAST searches employing known arthropod neuropeptide pre/preprohormone queries identified 49 transcripts as encoding putative homologs within the P. cavaticus transcriptome. The proteins deduced from these transcripts allowed for the prediction of 171 distinct mature neuropeptides. The P. cavaticus peptidome includes members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, leucokinin, myosuppressin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, sulfakinin, tachykinin-related peptide and trissin families, as well as many linker/precursor-related sequences that may or may not represent additional bioactive molecules. Interestingly, many of the predicted P. cavaticus neuropeptides possess structures identical (or nearly so) to those previously described from members of several other malacostracan orders, i.e., the Decapoda, Amphipoda and Euphausiacea, a finding that suggests broad phylogenetic conservation of bioactive peptide structures, and possibly functions, may exist within the Malacostraca.

Circadian signaling in the Northern krill Meganyctiphanes norvegica: In silico prediction of the protein components of a putative clock system using a publicly accessible transcriptome

The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn. In this and other euphausiids, an endogenous circadian pacemaker is thought, at least in part, to control DVM. Currently, there is no information concerning the identity of the genes/proteins that comprise the M. norvegica circadian system. In fact, there is little information concerning the molecular underpinnings of circadian rhythmicity in crustaceans generally. Here, a publicly accessible transcriptome was used to identify the molecular components of a putative Meganyctiphanes circadian system. A complete set of core clock proteins was deduced from the M. norvegica transcriptome (clock, cryptochrome 2, cycle, period and timeless), as was a large suite of proteins that likely function as modulators of the core clock (e.g., doubletime), or serves as inputs to it (cryptochrome 1) or outputs from it (pigment dispersing hormone). This is the first description of a "complete" (core clock through putative output pathway signals) euphausiid clock system, and as such, provides a foundation for initiating molecular investigations of circadian signaling in M. norvegica and other krill species, including how clock systems may regulate DVM and other behaviors.

Evaluation of ribosomal P0 peptide as a vaccine candidate against Argulus siamensis in Labeo rohita

Argulusspp. are important ectoparasites of fish, and the current approach of their control using chemical pesticides has numerous drawbacks. Vaccination is a promising alternative but identification of protective antigens is a limiting step. The ribosomal protein P0, essential for protein synthesis, has been studied as a vaccine candidate. We generated sequence information of the P0 protein of the ectoparasiteArgulus siamensisand the hostLabeo rohita. The region of the parasite P0 protein with less sequence similarity with that of the host P0 protein and high predicted antigenicity was used for peptide synthesis. The peptide was conjugated with keyhole limpet hemocyanin (KLH) for immunization of rohu at a dose of 1.5 μg/g body weight. Dot blot assays confirmed production of antibodies against pP0-KLH in immunized fish. We evaluated the efficiency of pP0-KLH as a vaccine antigen by challenge of the immunized fish withA.siamensis. Although there was no significant difference in parasite load between both groups, a reduced and delayed mortality of 59% (15 days post-infection) in immunized group was noticed as compared to 75% mortality (within 7–15 days post-infection) in control group. The partial protection observed indicated the need for further optimization of this molecule to develop it into a vaccine candidate.

The opsin repertoire of the Antarctic krill Euphausia superba

The Antarctic krill Euphausia superba experiences almost all marine photic environments throughout its life cycle. Antarctic krill eggs hatch in the aphotic zone up to 1000m depth and larvae develop on their way to the ocean surface (development ascent) and are exposed to different quality (wavelength) and quantity (irradiance) of light. Adults show a daily vertical migration pattern, moving downward during the day and upward during the night within the top 200m of the water column. Seawater acts as a potent chromatic filter and animals have evolved different opsin photopigments to perceive photons of specific wavelengths. We have investigated the transcriptome of E. superba and, using a candidate gene approach, we identified six novel opsins. Five are r-type visual opsins: four middle-wavelength-sensitive (EsRh2, EsRh3, EsRh4 and EsRh5) and one long-wavelength-sensitive (EsRh6). Moreover, we have identified a non-visual opsin, the EsPeropsin. All these newly identified opsin genes were significantly expressed in compound eyes and brain, while only EsPeropsin and EsRh2 were clearly detected also in the abdomen. A temporal modulation in the transcription of these novel opsins was found, but statistically significant oscillations were only observed in EsRrh3 and EsPeropsin. Our results contribute to the dissection of the complex photoreception system of E. superba, which enables this species to respond to the daily and seasonal changes in irradiance and spectral composition in the Southern Ocean.

De novo transcriptomic analysis of the female and male adults of the blood fluke Schistosoma turkestanicum

Background

Schistosoma turkestanicum is a parasite of considerable veterinary importance as an agent of animal schistosomiasis in many countries, including China. The S. turkestanicum cercariae can also infect humans, causing cercarial dermatitis in many countries and regions of the world. In spite of its significance as a pathogen of animals and humans, there is little transcriptomic and genomic data in the public databases.

Methods

Herein, we performed the transcriptome Illumina RNA sequencing (RNA-seq) of adult males and females of S. turkestanicum and de novo transcriptome assembly.

Results

Approximately 81.1 (female) and 80.5 (male) million high-quality clean reads were obtained and then 29,526 (female) and 41,346 (male) unigenes were assembled. A total of 34,624 unigenes were produced from S. turkestanicum females and males, with an average length of 878 nucleotides (nt) and N50 of 1480 nt. Of these unigenes, 25,158 (72.7 %) were annotated by blast searches against the NCBI non-redundant protein database. Among these, 21,995 (63.5 %), 22,189 (64.1 %) and 13,754 (39.7 %) of the unigenes had significant similarity in the NCBI non-redundant protein (NR), non-redundant nucleotide (NT) and Swiss-Prot databases, respectively. In addition, 3150 unigenes were identified to be expressed specifically in females and 1014 unigenes were identified to be expressed specifically in males. Interestingly, several pathways associated with gonadal development and sex maintenance were found, including the Wnt signaling pathway (103; 2 %) and progesterone-mediated oocyte maturation (77; 1.5 %).

Conclusions

The present study characterized and compared the transcriptomes of adult female and male blood fluke, S. turkestanicum. These results will not only serve as valuable resources for future functional genomics studies to understand the molecular aspects of S. turkestanicum, but also will provide essential information for ongoing whole genome sequencing efforts on this pathogenic blood fluke.

Identification and characterisation of hemocyanin of the fish louse Argulus (Crustacea: Branchiura)

Hemocyanin transports oxygen in the hemolymph of many arthropod species. Within the crustaceans, this copper-containing protein was thought to be restricted to Malacostraca, while other crustacean classes were assumed to employ hemoglobin or lack any respiratory protein. Only recently it has become evident that hemocyanins also occur in Remipedia and Ostracoda. Here we report for the first time the identification and characterisation of hemocyanin in the fish louse Argulus, which belongs to the class of Branchiura. This finding indicates that hemocyanin was the principal oxygen carrier in the stem lineage of the pancrustaceans, but has been lost independently multiple times in crustacean taxa. We obtained the full-length cDNA sequences of two hemocyanin subunits of Argulus foliaceus by a combination of RT-PCR, RACE and Illumina sequencing of the transcriptome. In addition, one full-length and one partial cDNA sequence were derived from the transcriptome data of Argulus siamensis. Western blot analysis confirmed the presence of at least two hemocyanin subunits in A. foliaceus, which are expressed at the mRNA level at a 1:3.5 ratio. The addition to the branchiuran hemocyanin subunits to a multiple sequence alignment of arthropod, hemocyanins improved the phylogenetic resolution within the pancrustacean hemocyanins. Malacostracan, ostracod and branchiuran hemocyanins are distinct from the hexapod and remipede hemocyanins, reinforcing the hypothesis of a close relationship of Remipedia and Hexapoda. Notably, the ostracod hemocyanins are paraphyletic with respect to the branchiuran hemocyanins, indicating ancient divergence and differential loss of distinct subunit types.

Peptide discovery in the ectoparasitic crustacean Argulus siamensis: identification of the first neuropeptides from a member of the Branchiura

Recent advances in high-throughput sequencing have facilitated the generation of large transcriptomic datasets for an ever-growing number of crustaceans, one being the carp louse Argulus siamensis. This and other members of the subclass Branchiura are obligate fish ectoparasites, and as such, are a major concern for commercial aquaculture. Using the extant transcriptome shotgun assembly (TSA) sequences for A. siamensis, 27 transcripts encoding putative neuropeptide precursors were identified, and their pre/preprohormones deduced and characterized using a well-established bioinformatics workflow. The structures of 105 distinct peptides were predicted from the deduced proteins, including isoforms of adipokinetic hormone (AKH), allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, crustacean cardioactive peptide (CCAP), diuretic hormone 31, diuretic hormone 44, eclosion hormone, myosuppressin, neuroparsin, neuropeptide Y, orcokinin, pigment dispersing hormone, proctolin, short neuropeptide F, SIFamide, sulfakinin and tachykinin-related peptide. While several of the predicted peptides are known from other crustacean and/or insect species, e.g. RYLPT, a broadly conserved arthropod proctolin isoform, and PFCNAFTGCamide (disulfide bridging between the two cysteines), the stereotypical crustacean CCAP, the vast majority of them are described here for the first time, e.g. pQVNFSTKWamide, a new AKH/red pigment concentrating hormone superfamily member, pQEGLDHMFMRFamide, a novel myosuppressin, and SYKSKPPFNGSIFamide, a new member of the SIFamide family. As the peptides presented here are the only ones thus far described from A. siamensis, or for that matter, any branchiuran, they represent a new resource to begin investigations of peptidergic control of physiology and behavior in this and other related aquacultural pests.

TLR and IMD signaling pathways from Caligus rogercresseyi (Crustacea: Copepoda): in silico gene expression and SNPs discovery

The Toll and IMD signaling pathways represent one of the first lines of innate immune defense in invertebrates like Drosophila. However, for crustaceans like Caligus rogercresseyi, there is very little genomic information and, consequently, understanding of immune mechanisms. Massive sequencing data obtained for three developmental stages of C. rogercresseyi were used to evaluate in silico the expression patterns and presence of SNPs variants in genes involved in the Toll and IMD pathways. Through RNA-seq analysis, which used 20 contigs corresponding to relevant genes of the Toll and IMD pathways, an overexpression of genes linked to the Toll pathway, such as toll3 and Dorsal, were observed in the copepod stage. For the chalimus and adult stages, overexpression of genes in both pathways, such as Akirin and Tollip and IAP and Toll9, respectively, were observed. On the other hand, PCA statistical analysis inferred that in the chalimus and adult stages, the immune response mechanism was more developed, as evidenced by a relation between these two stages and the genes of both pathways. Moreover, 136 SNPs were identified for 20 contigs in genes of the Toll and IMD pathways. This study provides transcriptomic information about the immune response mechanisms of Caligus, thus providing a foundation for the development of new control strategies through blocking the innate immune response.