Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique

Nucleic Acid Sensing by STING Induces an IFN-like Antiviral Response in a Marine Invertebrate

The cytosolic detection of pathogen-derived nucleic acids has evolved as an essential strategy for host innate immune defense in mammals. One crucial component in this process is the stimulator of IFN genes (STING), which acts as a vital signaling adaptor, connecting the cytosolic detection of DNA by cyclic GMP-AMP (cGAMP) synthase (cGAS) to the downstream type I IFN signaling pathway. However, this process remains elusive in invertebrates. In this study, we present evidence demonstrating that STING, an ortholog found in a marine invertebrate (shrimp) called Litopenaeus vannamei, can directly detect DNA and initiate an IFN-like antiviral response. Unlike its homologs in other eukaryotic organisms, which exclusively function as sensors for cyclic dinucleotides, shrimp STING has the ability to bind to both double-stranded DNA and cyclic dinucleotides, including 2'3'-cGAMP. In vivo, shrimp STING can directly sense DNA nucleic acids from an infected virus, accelerate IFN regulatory factor dimerization and nuclear translocation, induce the expression of an IFN functional analog protein (Vago4), and finally establish an antiviral state. Taken together, our findings unveil a novel double-stranded DNA-STING-IKKε-IRF-Vago antiviral axis in an arthropod, providing valuable insights into the functional origins of DNA-sensing pathways in evolution.

Genome-wide association study identified genes associated with ammonia nitrogen tolerance in Litopenaeus vannamei

Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L. vannamei. These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L. vannamei. Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei. Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei.

Identification of Hox genes and their expression profiles during embryonic development of the emerging model organism, Macrobrachium olfersii

Hox genes encode transcription factors that specify the body segment identity during development, including crustaceans, such as amphipods and decapods, that possess a remarkable diversity of segments and specialized appendages. In amphipods, alterations of specialized appendages have been obtained using knockout experiment of Hox genes, which suggests that these genes are involved in the evolution of morphology within crustaceans. However, studies of Hox genes in crustaceans have been limited to a few species. Here, we identified the homeodomain of nine Hox genes: labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abdA), and Abdominal-B (AbdB), and evaluated their expression by RT-qPCR and RT-PCR in the ovary, during embryonic development, and at the first larval stage (Zoea I) of the decapod Macrobrachium olfersii. The transcript levels of lab, Dfd, and ftz decreased and transcripts of pb, Scr, Antp, Ubx, abdA, and AbdB increased during embryonic development. Hox genes were expressed in mature ovaries and Zoea I larval stages, except Scr and ftz, respectively. In addition, isoforms of Dfd, Scr, Ubx, and abdA, which have been scarcely reported in crustaceans, were described. New partial sequences of 87 Hox genes from other crustaceans were identified from the GenBank database. Our results are interesting for future studies to determine the specific function of Hox genes and their isoforms in the freshwater prawn M. olfersii and to contribute to the understanding of the diversity and evolution of body plans and appendages in Crustaceans.

Interferon-Induced Protein 6-16 (IFI6-16) from Litopenaeus vannamei Regulate Antiviral Immunity via Apoptosis-Related Genes

A growing number of evidence shows that some invertebrates possess an antiviral immunity parallel to the interferon (IFN) system of higher vertebrates. For example, the IRF (interferon regulatory factor)–Vago–JAK/STAT regulatory axis in an arthropod, shrimp Litopenaeus vannamei (whiteleg shrimp) is functionally similar to the IRF–IFN–JAK/STAT axis of mammals. IFNs perform their cellular immunity by regulating the expression of target genes collectively referred to as IFN-stimulated genes (ISGs). However, the function of invertebrate ISGs in immune responses is almost completely unclear. In this study, a potential ISG gene homologous to the interferon-induced protein 6-16 (IFI6-16) was cloned and identified from L. vannamei, designated as LvIFI6-16. LvIFI6-16 contained a putative signal peptide in the N-terminal, and a classic IFI6-16-superfamily domain in the C-terminal that showed high conservation to other homologs in various species. The mRNA levels of LvIFI6-16 were significantly upregulated after the stimulation of poly (I:C) and challenges of white spot syndrome virus (WSSV). Moreover, silencing of LvIFI6-16 caused a higher mortality rate and heightened virus loads, suggesting that LvIFI6-16 could play a crucial role in defense against WSSV. Interestingly, we found that the transcription levels of several caspases were regulated by LvIFI6-16; meanwhile, the transcription level of LvIFI6-16 self was regulated by the JAK/STAT cascade, suggesting there could be a JAK/STAT–IFI6-16–caspase regulatory axis in shrimp. Taken together, we identified a crustacean IFI6-16 gene (LvIFI6-16) for the first time, and provided evidence that the IFI6-16 participated in antiviral immunity in shrimp.

Isolation, identification and phylogenetic analysis of lumpy skin disease virus strain of outbreak in Guangdong, China

In August 2019, Lumpy skin disease broke out for the first time in Xinjiang, China, and then quickly spread to many provinces in China. Here, the virus was isolated from the skin scabs of affected cattle during June 2020 in Guangdong, China. Virus isolation, transmission electron microscopy and polymerase chain reaction identified lumpy skin disease virus (LSDV) in the skin crusts of sick cattle. For the isolation of LSDV, the most sensitive cell line is primary cattle testicular (PCT) cells, while Vero cells cannot be used for the isolation of LSDV. In addition, we evaluated the growth characteristics of LSDV. Compared with MDBK and Vero cells, LSDV produced the higher virus titers in PCT cells at 72 h. Phylogenetic analysis based on second-generation sequencing of the LSDV whole genome showed that the isolated virus (LSDV/MZGD/2020) is closely related to Asian strains and formed a new branch. LSDV/MZGD/2020 is also a vaccine recombinant strain, which is distinct from the recombinant strain found in Russia. Through RDP (Recombination Detection Program), Simplot and phylogenetic analyses, strong evidence for recombination events were found in Chinese field LSDV strains. The China LSDV/MZGD/2020 strain may be the result of multiple recombination events between the Neethling 2490 and Neethling vaccine LW 1959 strains. This study expanded our knowledge on the genetic diversity and evolution of LSDV. This article is protected by copyright. All rights reserved.

RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (Litopenaeus vannamei) in Different Stages of Development

White leg shrimp (Litopenaeus vannamei) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of L. vannamei has been previously studied in different developmental stages, but there is limited information regarding the functional role of the microbiome during the development of L. vannamei. In this study the metatranscriptome in different developmental stages of L. vannamei (larvae, juvenile and adult) were generated using next generation sequencing techniques. The bacterial phyla found throughout all the stages of development belonged to the Proteobacteria, Firmicutes and Actinobacteria, these bacterial phyla are present in the digestive tract and are capable of producing several hydrolytic enzymes, which agrees with high representation of the primary metabolism and energy production, in both host and the microbiome. In this sense, functional changes were observed as the development progressed, in both host and the microbiome, in stages of larvae the most represented metabolic functions were associated with biomass production; while in juvenile and adult stages a higher proportion of metabolic functions associated to biotic and abiotic stress in L. vannamei and the microbiome were shown. This study provides evidence of the interaction of the microbiome with L. vannamei, and how the stage of development and the culture conditions of this species influences the gene expression and the microbiome composition, which suggests a complex metabolic network present throughout the life cycle of L. vannamei.

Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa)

BACKGROUND

Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mechanisms underlying gonad development and gametogenesis remain unclear in Tridacna squamosa, a large-size bivalve of great ecological value. They are protandrous simultaneous hermaphrodites, with the male gonad maturing first, eventually followed by the female gonads. In this study, nine gonad libraries representing resting, male and hermaphrodite stages in T. squamosa were performed to identify the molecular mechanisms.

RESULTS

Sixteen thousand four hundred ninety-one unigenes were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 5091 and 7328 unigenes were assigned to Gene Ontology categories and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database, respectively. A total of 4763 differentially expressed genes (DEGs) were identified by comparing male to resting gonads, consisting of 3499 which were comparatively upregulated in males and 1264 which were downregulated in males. Six hundred-ninteen DEGs between male and hermaphroditic gonads were identified, with 518 DEGs more strongly expressed in hermaphrodites and 101 more strongly expressed in males. GO (Gene Ontology) and KEGG pathway analyses revealed that various biological functions and processes, including functions related to the endocrine system, oocyte meiosis, carbon metabolism, and the cell cycle, were involved in regulating gonadal development and gametogenesis in T. squamosa. Testis-specific serine/threonine kinases 1 (TSSK1), TSSK4, TSSK5, Doublesex- and mab-3-related transcription factor 1 (DMRT1), SOX, Sperm surface protein 17 (SP17) and other genes were involved in male gonadal development in Tridacna squamosal. Both spermatogenesis- (TSSK4, spermatogenesis-associated protein 17, spermatogenesis-associated protein 8, sperm motility kinase X, SP17) and oogenesis-related genes (zona pellucida protein, Forkhead Box L2, Vitellogenin, Vitellogenin receptor, 5-hydroxytryptamine, 5-hydroxytryptamine receptor) were simultaneously highly expressed in the hermaphroditic gonad to maintain the hermaphroditism of T. squamosa.

CONCLUSION

All these results from our study will facilitate better understanding of the molecular mechanisms underlying giant clam gonad development and gametogenesis, which can provided a base on obtaining excellent gametes during the seed production process for giant clams.

Penaeidins restrict white spot syndrome virus infection by antagonizing the envelope proteins to block viral entry

Emerging studies have indicated that some penaeidins restrict virus infection; however, the mechanism(s) involved are poorly understood. In the present study, we uncovered that penaeidins are a novel family of antiviral effectors against white spot syndrome virus (WSSV), which antagonize the envelope proteins to block viral entry. We found that the expression levels of four identified penaeidins from Litopenaeus vannamei, including BigPEN, PEN2, PEN3, and PEN4, were significantly induced in hemocytes during the early stage of WSSV infection. Knockdown of each penaeidin in vivo via RNA interference resulted in elevated viral loads and rendered shrimp more susceptible to WSSV, while the survival rate was rescued via the injection of recombinant penaeidins. All penaeidins, except PEN4, were shown to interact with several envelope proteins of WSSV, and all four penaeidins were observed to be located on the outer surface of the WSSV virion. Co-incubation of each recombinant penaeidin with WSSV inhibited virion internalization into hemocytes. More importantly, we found that PEN2 competitively bound to the envelope protein VP24 to release it from polymeric immunoglobulin receptor (pIgR), the cellular receptor required for WSSV infection. Moreover, we also demonstrated that BigPEN was able to bind to VP28 of WSSV, which disrupted the interaction between VP28 and Rab7 – the Rab GTPase that contributes to viral entry by binding with VP28. Taken together, our results demonstrated that penaeidins interact with the envelope proteins of WSSV to block multiple viral infection processes, thereby protecting the host against WSSV.

Ecdysis triggering hormone modulates molt behaviour in the redclaw crayfish Cherax quadricarinatus, providing a mechanistic evidence for conserved function in molt regulation across Pancrustacea

Molting enables growth and development across ecdysozoa. The molting process is strictly controlled by hormones - ecdysteroids. Ecdysteroidogenesis occurs in theprothoracic glands and stimulated by prothoracicotropic hormone in insects, while it ensues in the Y-organ and regulated by the molt inhibiting hormone in crustaceans. A peak in ecdysteroids in the hemolymph induces a cascade of multiple neuropeptides including Ecdysis Triggering Hormone (ETH) and Corazonin. The role of ETH is well defined in controlling the molt process in insects, but it is yet to be defined in crustaceans. In this study, we investigated the behavioral response of intermolt crayfish to ETH and Corazonin injections as well as the impact of ETH on the molt period using in vivo assays. Injection of Corazonin and ETH resulted in a clear and immediate eye twitching response to these two neuropeptides. The Corazonin injection induced eye twitching in slow and asynchronous manner, while ETH injection caused eye twitching in a relatively fast and synchronous way. A single injection of ETH to crayfish resulted in a remarkable prolong molt period, at twice the normal molting cycle, suggesting that ETH plays a key role in controlling the molt cycle in decapod crustaceans. Given the key significance of ETH in molt regulation and its plausible application in pest control, we characterized ETH across the pancrustacean orders. Bioinformatic analysis shows the mature ETH sequence is identical in all studied decapod species. ETH can be classified into specific groups based on the associated motif in each insect order and shows an insect motif -KxxPRx to be conserved in crustaceans.

TNF-Receptor-Associated Factor 3 in Litopenaeus vannamei Restricts White Spot Syndrome Virus Infection Through the IRF-Vago Antiviral Pathway

Tumor necrosis factor receptor (TNFR)-associated factors (TRAFs) are vital signaling adaptor proteins for the innate immune response and are involved in many important pathways, such as the NF-κB- and interferon regulatory factor (IRF)-activated signaling pathways. In this study, the TRAF3 ortholog from the shrimp Litopenaeus vannamei (LvTRAF3) was cloned and characterized. LvTRAF3 has a transcript of 3,865 bp, with an open reading frame (ORF) of 1,002 bp and encodes a polypeptide of 333 amino acids, including a conserved TRAF-C domain. The expression of LvTRAF3 in the intestine and hemocyte was up-regulated in response to poly (I:C) challenge and white spot syndrome virus (WSSV) infection. RNAi knockdown of LvTRAF3 in vivo significantly increased WSSV gene transcription, viral loads, and mortality in WSSV-infected shrimp. Next, we found that LvTRAF3 was not able to induce the activation of the NF-κB pathway, which was crucial for synthesis of antimicrobial peptides (AMPs), which mediate antiviral immunity. Specifically, in dual-luciferase reporter assays, LvTRAF3 could not activate several types of promoters with NF-κB binding sites, including those from WSSV genes (wsv069, wsv056, and wsv403), Drosophila AMPs or shrimp AMPs. Accordingly, the mRNA levels of shrimp AMPs did not significantly change when TRAF3 was knocked down during WSSV infection. Instead, we found that LvTRAF3 signaled through the IRF-Vago antiviral cascade. LvTRAF3 functioned upstream of LvIRF to regulate the expression of LvVago4 and LvVago5 during WSSV infection in vivo. Taken together, these data provide experimental evidence of the participation of LvTRAF3 in the host defense to WSSV through the activation of the IRF-Vago pathway but not the NF-κB pathway.

De Novo Transcriptome Assembly and Gene Expression Profiling of the Copepod Calanus helgolandicus Feeding on the PUA-Producing Diatom Skeletonema marinoi

Diatoms are the dominant component of the marine phytoplankton. Several diatoms produce secondary metabolites, namely oxylipins, with teratogenic effects on their main predators, crustacean copepods. Our study reports the de novo assembled transcriptome of the calanoid copepod Calanus helgolandicus feeding on the oxylipin-producing diatom Skeletonema marinoi. Differential expression analysis was also performed between copepod females exposed to the diatom and the control flagellate Prorocentrum minimum, which does not produce oxylipins. Our results showed that transcripts involved in carbohydrate, amino acid, folate and methionine metabolism, embryogenesis, and response to stimulus were differentially expressed in the two conditions. Expression of 27 selected genes belonging to these functional categories was also analyzed by RT-qPCR in C. helgolandicus females exposed to a mixed solution of the oxylipins heptadienal and octadienal at the concentration of 10 µM, 15 µM, and 20 µM. The results confirmed differential expression analysis, with up-regulation of genes involved in stress response and down-regulation of genes associated with folate and methionine metabolism, embryogenesis, and signaling. Overall, we offer new insights on the mechanism of action of oxylipins on maternally-induced embryo abnormality. Our results may also help identify biomarker genes associated with diatom-related reproductive failure in the natural copepod population at sea.

Transcriptome Analysis Reveals the Tolerance Mechanism of Mantis Shrimp (Oratosquilla oratoria) under a Lipopolysaccharide Challenge

Lipopolysaccharide (LPS), a major cell wall component of Gram-negative bacteria, is considered to lead to some disease development in commercial crustaceans. However, mantis shrimps Oratosquilla oratoria (Crustacea: Stomatopoda) have a strong vitality and ability to resist disease. To study the tolerance mechanism of mantis shrimp, transcriptome analyses were conducted in hepatopancreas of O. oratoria under LPS challenge investigation. Totally, 84 547 044 clean reads were obtained from transcriptomes (43 159 230 in OP (control), 41 387 814 in OL (treatment), respectively). Unigenes, the longest transcript of each gene, with a total length of 68 318 880 bp and the total number of 100 978 were obtained. 8369 (8.28%) of unigenes were successfully annotated in all databases and 54 888 (54.35%) were annotated in at least one database. Finally, 1012 differentially expressed genes (DEGs) including 439 and 573 showed significantly upregulated and downregulated were determined between OL and OP, respectively. Moreover, those DEGs only expressed in OL or OP accounted for 8.99%. The functional classification based on GO and KEGG indicated that the common enrichment categories for the DEGs are "amino sugar metabolic" and "cellular homeostasis" and that the progress of nutrient metabolic and homeostasis in cells is important in facing variable environmental conditions. Protein-protein interaction analysis elucidated proteins, β-actin (ACTB_G1), T-complex protein subunits (TCPs), heat shock proteins (HSPs), hydroxysteroid dehydrogenase-like protein 2 (HSDL2), kinesin family member 5 (KIF5), methylglutaconyl-CoA hydratase (AUH), and myosin heavy chain (MYH) may play key roles in response to an LPS challenge. This study laid a foundation to further investigate the possible adaptation way that O. oratoria survives in a bacterial challenge.

Ovarian Transcriptomic Analyses in the Urban Human Health Pest, the Western Black Widow Spider

Due to their abundance and ability to invade diverse environments, many arthropods have become pests of economic and health concern, especially in urban areas. Transcriptomic analyses of arthropod ovaries have provided insight into life history variation and fecundity, yet there are few studies in spiders despite their diversity within arthropods. Here, we generated a de novo ovarian transcriptome from 10 individuals of the western black widow spider (Latrodectus hesperus), a human health pest of high abundance in urban areas, to conduct comparative ovarian transcriptomic analyses. Biological processes enriched for metabolism—specifically purine, and thiamine metabolic pathways linked to oocyte development—were significantly abundant in L. hesperus. Functional and pathway annotations revealed overlap among diverse arachnid ovarian transcriptomes for highly-conserved genes and those linked to fecundity, such as oocyte maturation in vitellogenin and vitelline membrane outer layer proteins, hormones, and hormone receptors required for ovary development, and regulation of fertility-related genes. Comparative studies across arachnids are greatly needed to understand the evolutionary similarities of the spider ovary, and here, the identification of ovarian proteins in L. hesperus provides potential for understanding how increased fecundity is linked to the success of this urban pest.

Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation

Background

Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on how M. rosenbergii post-larvae launches an immune response to an infection with MrNV is not currently available. We therefore compared the whole transcriptomic sequence of M. rosenbergii post-larvae before and after MrNV infection.

Results

Transcriptome for M. rosenbergii post-larvae demonstrated high completeness (BUSCO Complete: 83.4%, fragmentation: 13%, missing:3.3%, duplication:16.2%; highest ExN50 value: 94%). The assembled transcriptome consists of 96,362 unigenes with N₅₀ of 1308 bp. The assembled transcriptome was successfully annotated against the NCBI non-redundant arthropod database (33.75%), UniProt database (26.73%), Gene Ontology (GO) (18.98%), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG) (20.88%), and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) (20.46%). GO annotations included immune system process, signaling, response to stimulus, and antioxidant activity. Differential abundance analysis using EdgeR showed 2413 significantly up-regulated genes and 3125 significantly down-regulated genes during the infection of MrNV.

Conclusions

This study reported a highly complete transcriptome from the post-larvae stage of giant river prawn, M. rosenbergii. Differential abundant transcripts during MrNV infection were identified and validated by qPCR, many of these differentially abundant transcripts as key players in antiviral immunity. These include known members of the innate immune response with the largest expression change occurring in the M. rosenbergii post-larvae after MrNV infection such as antiviral protein, C-type lectin, prophenol oxidase, caspase, ADP ribosylation factors, and dicer.

Single-molecule long-read sequencing facilitates shrimp transcriptome research

Although shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We obtained 322,600 full-length non-chimeric reads, from which we generated 51,367 high-quality unique full-length transcripts. We corrected errors in the SMRT sequences by comparison with Illumina-produced short reads. We successfully annotated 81.72% of all unique SMRT transcripts against the NCBI non-redundant database, 58.63% against Swiss-Prot, 45.38% against Gene Ontology, 32.57% against Clusters of Orthologous Groups of proteins (COG), and 47.83% against Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Across all transcripts, we identified 3,958 long non-coding RNAs (lncRNAs) and 80,650 simple sequence repeats (SSRs). Our study provides a rich set of full-length cDNA sequences for L. vannamei, which will greatly facilitate shrimp transcriptome research.

RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides

The function of Toll pathway defense against bacterial infection has been well established in shrimp, however how this pathway responds to viral infection is still largely unknown. In this study, we report the Toll4-Dorsal-AMPs cascade restricts the white spot syndrome virus (WSSV) infection of shrimp. A total of nine Tolls from Litopenaeus vannamei namely Toll1-9 are identified, and RNAi screening in vivo reveals the Toll4 is important for shrimp to oppose WSSV infection. Knockdown of Toll4 results in elevated viral loads and renders shrimp more susceptible to WSSV. Furthermore, Toll4 could be a one of upstream pattern recognition receptor (PRR) to detect WSSV, and thereby leading to nuclear translocation and phosphorylation of Dorsal, the known NF-κB transcription factor of the canonical Toll pathway. More importantly, silencing of Toll4 and Dorsal contributes to impaired expression of a specific set of antimicrobial peptides (AMPs) such as anti-LPS-factor (ALF) and lysozyme (LYZ) family, which exert potent anti-WSSV activity. Two AMPs of ALF1 and LYZ1 as representatives are demonstrated to have the ability to interact with several WSSV structural proteins to inhibit viral infection. Taken together, we therefore identify that the Toll4-Dorsal pathway mediates strong resistance to WSSV infection by inducing some specific AMPs.

The TLR pathway mediated antiviral immune response is well identified in mammals, yet, Toll pathway governing this protection in invertebrates remains unknown. In the present study, we uncover that a shrimp Toll4 from a total of nine Tolls in L. vannamei confers resistance to WSSV thought inducing the NF-κB transcription factor Dorsal to inspire the production of some antimicrobial peptides (AMPs) with antiviral activity. The anti-LPS-factor (ALF) and lysozyme (LYZ) family are identified as the Toll4-Dorsal pathway targeted genes with the ability to interact with viral structural proteins in response to WSSV infection. These results suggest that the Toll receptor induces the expression of AMPs with antiviral activity could be a general antiviral mechanism in invertebrates and Toll pathway established antiviral defense could be conserved during evolution.

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.

Comparative transcriptome analysis of Eriocheir japonica sinensis response to environmental salinity

Chinese mitten crabs (Eriocheir japonica sinensis) are catadromous, spending most of their lives in fresh water, but moving to a mixed salt-fresh water environment for reproduction. The characteristics of this life history might imply a rapidly evolutionary transition model for adaptation to marine from freshwater habitats. In this study, transcriptome-wide identification and differential expression on Chinese mitten crab groups were analysed. Results showed: clean reads that were obtained totalled 93,833,096 (47,440,998 in Group EF, the reference, and 46,392,098 in Group ES, the experimental) and 14.08G (7.12G in Group EF 6.96G in Group ES); there were 11,667 unigenes (15.29%) annotated, and they were located to 230 known KEGG pathways in five major categories; in differential expression analysis, most of the top 20 up-regulated pathways were connected to the immune system, disease, and signal transduction, while most of the top 20 down-regulated pathways were related to the metabolism system; meanwhile, 8 representative osmoregulation-related genes (14-3-3 epsilon, Cu2+ transport ATPase, Na+/K+ ATPase, Ca2+ transporting ATPase, V-ATPase subunit A, Putative arsenite-translocating ATPase, and Cation transport ATPase, Na+/K+ symporter) showed up-regulation, and 1 osmoregulation-related gene (V-ATPase subunit H) showed down-regulation. V-ATPase subunit H was very sensitive to the transition of habitats. These results were consistent with the tests of qRT-PCR. The present study has provided a foundation to further understand the molecular mechanism in response to salinity changing in water.

The State of "Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.

A transcriptome study on Macrobrachium nipponense hepatopancreas experimentally challenged with white spot syndrome virus (WSSV)

White spot syndrome virus (WSSV) is one of the most devastating pathogens of cultured shrimp, responsible for massive loss of its commercial products worldwide. The oriental river prawn Macrobrachium nipponense is an economically important species that is widely farmed in China and adult prawns can be infected by WSSV. However, the molecular mechanisms of the host pathogen interaction remain unknown. There is an urgent need to learn the host pathogen interaction between M. nipponense and WSSV which will be able to offer a solution in controlling the spread of WSSV. Next Generation Sequencing (NGS) was used in this study to determin the transcriptome differences by the comparison of control and WSSV-challenged moribund samples, control and WSSV-challenged survived samples of hepatopancreas in M. nipponense. A total of 64,049 predicted unigenes were obtained and classified into 63 functional groups. Approximately, 4,311 differential expression genes were identified with 3,308 genes were up-regulated when comparing the survived samples with the control. In the comparison of moribund samples with control, 1,960 differential expression genes were identified with 764 genes were up-regulated. In the contrast of two comparison libraries, 300 mutual DEGs with 95 up-regulated genes and 205 down-regulated genes. All the DEGs were performed GO and KEGG analysis, overall a total of 85 immune-related genes were obtained and these gene were groups into 13 functions and 4 KEGG pathways, such as protease inhibitors, heat shock proteins, oxidative stress, pathogen recognition immune receptors, PI3K/AKT/mTOR pathway, MAPK signaling pathway and Ubiquitin Proteasome Pathway. Ten genes that valuable in immune responses against WSSV were selected from those DEGs to furture discuss the response of host to WSSV. Results from this study contribute to a better understanding of the immune response of M. nipponense to WSSV, provide information for identifying novel genes in the absence of genome of M. nipponense. Furthermore, large number of transcripts obtained from this study could provide a strong basis for future genomic research on M. nipponense.

Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp ( Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Cr (VI), the pathogenicity factor, is widely known to cause toxic effects in living organisms. Given the economic importance of the mantis shrimp ( Oratosquilla oratoria), the understanding of impacts by Cr (VI) is considered important. In this study, transcriptome of mantis shrimp was characterized by a comparison between control and Cr (VI)-treated samples using RNA-seq approach. Totally, 88 234 826 bp and 13.24G clean reads were obtained. The total length and number of unigenes were 68 411 206 bp and 100 918, respectively. The maximal and average length of unigenes was 24 906 bp and 678 bp, respectively (N50, 798 bp). 7115 of these unigenes accounted for 7.05% of the total that were annotated in all databases. After annotation of assembled unigenes, 35 619 of them were assigned into 3 functional categories and 56 subcategories using Gene Ontology; 18 580 of them were assigned into 26 functional categories using Clusters of Orthologous Groups of proteins; 16 864 of them were assigned into 5 major categories and 32 subclasses using KEGG. Finally, 1730 genes were differentially expressed (DGEs), 9 up-regulated pathways (protein digestion and absorption, neuroactive ligand-receptor interaction, pancreatic secretion, tyrosine metabolism, amoebiasis, ECM-receptor interaction, riboflavin metabolism, amino sugar and nucleotide sugar metabolism and AGE-RAGE signaling pathway in diabetic complications) were significantly enriched ( q < 0.05), and one down-regulated pathway ( Staphylococcus aureus infection) was significantly enriched ( q < 0.05). Up-regulation of genes in pathways of protein digestion/absorption ( PepT1/SLC15A and ATP1B) and environment information processing ( COL1AS, COL4A; LAMA3_5, LAMB3; FN1 and TN) may imply the potentially positive toxicity resistance mechanisms.

A molting-inhibiting hormone-like protein from Pacific white shrimp Litopenaeus vannamei is involved in immune responses

The molting-inhibiting hormones (MIHs) from the crustacean hyperglycemic hormone (CHH) family are a group of neuropeptides that are implicated in regulation of molting and reproduction in crustaceans. In this study, a novel protein containing a typical crustacean neuropeptide domain was identified from Litopenaeus vannamei. The protein showed high homology with other shrimp MIHs and was then designated as a MIH-like protein (MIHL). Among the detected tissues, the heart expressed the highest level of MIHL. The expression of MIHL could be significantly up-regulated after infection with white spot syndrome virus (WSSV), gram-negative bacterium Vibro parahaemolyticus and gram-positive bacterium Staphylococcus aureus, indicating that MIHL could be involved in immune responses. The promoter of MIHL was predicted to contain two NF-κB binding sites and could be regulated by the NF-κB family protein Relish but not Dorsal, suggesting that MIHL could be an effector gene of the IMD/Relish pathway. Silencing of MIHL in vivo by RNAi strategy significantly down-regulated the expression of many immune effector genes and increased the mortalities of shrimp infected by V. parahaemolyticus and WSSV and their copy numbers in tissues. These confirmed that MIHL could play a role in antiviral and antibacterial immune responses in shrimp.

MKK4 from Litopenaeus vannamei is a regulator of p38 MAPK kinase and involved in anti-bacterial response

LvMKK4, a homologue of the mammalian mitogen-activated protein kinase kinase 4 (MKK4), was isolated and identified from Litopenaeus vannamei in the present study. The full-length cDNA of LvMKK4 is 1947 bp long, with an open reading frame (ORF) of 1185 bp encoding a putative protein of 388 amino acids. LvMKK4 contains several characteristic domains such as D domain, SIAKT motif and kinase domain, all of which are conserved in MAP kinase kinase family. Like mammalian MKK4 but not Drosophila MKK4, LvMKK4 could bind to, phosphorylate and activate p38 MAPK, which provided some insights into the signal transduction mechanism of MKK4-p38 cascade in invertebrates. Our real-time PCR data indicated that LvMKK4 was ubiquitously expressed in all tested tissues and extraordinarily abundant in muscle. Dual luciferase reporter assays in Drosophila S2 cells revealed that LvMKK4 activated the transcription of antimicrobial peptide genes (AMPs), including Drosophila Attacin A, Drosomycin, and shrimp Penaeidins. Additionally, LvMKK4 was up-regulated in both intestine and hepatopancreas by a variety of inflammatory stimuli including LPS, Vibrio parahaemolyticus, Staphhylococcu saureus, Poly (I: C) and white spot syndrome virus. Furthermore, RNAi-mediated knockdown of LvMKK4 enhanced the sensitivity of L. vannamei to V. parahaemolyticus infection. These findings suggested that LvMKK4 played an important role in anti-bacterial response and could be a potential target for inflammation treatment.

Transcriptome sequencing and differential gene expression analysis of the schistosome-transmitting snail Oncomelania hupensis inhabiting hilly and marshland regions

The freshwater snail Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which is the major cause of schistosomiasis. The snail inhabits two contrasting environments: the hilly and marshland regions. The hilly snails are smaller in size and have the typical smooth shell, whereas the marshland snails are larger and possess the ribbed shell. To reveal the differences in gene expression between the hilly and marshland snails, a total of six snails, three per environment, were individually examined by RNA sequencing technology. All paired-end reads were assembled into contigs from which 34,760 unigenes were predicted. Based on single nucleotide polymorphisms, principal component analysis and neighbor-joining clustering revealed two distinct clusters of hilly and marshland snails. Analysis of expression changes between environments showed that upregulated genes relating to immunity and development were enriched in hilly snails, while those associated with reproduction were over-represented in marshland snails. Eight differentially expressed genes between the two types of snails were validated by qRT-PCR. Our study identified candidate genes that could be targets for future functional studies, and provided a link between expression profiling and ecological adaptation of the snail that may have implications for schistosomiasis control.

Identification, characterization, and function analysis of the NF-κB repressing factor (NKRF) gene from Litopenaeus vannamei

The NF-κB family transcription factors regulate a wide spectrum of biological processes, in particular immune responses. The studies in human suggest that the NF-κB repressing factor (NKRF) negatively regulates the activity of NF-κB through a direct protein-protein interaction. However, the function of NKRF has not been studied outside mammals up to now. The current study identified a NKRF gene (LvNKRF) from the Pacific white shrimp, Litopenaeus vannamei, which showed homology with NKRFs from insects, fishes and mammals. LvNKRF was high expressed in intestine, stomach and muscle tissues and was localized in the nucleus. LvNKRF could interact with both Dorsal and Relish, the two members of the shrimp NF-κB family. Interestingly, although sharing a similar protein structure with that of human NKRF, LvNKRF showed no inhibitory but instead enhancing effects on activities of Dorsal and Relish, which was contrary to those of mammalian NKRFs. The expression of LvNKRF could not be induced by Gram-positive and -negative bacteria and immunostimulants lipopolysaccharide (LPS) and poly (I:C) but was significantly up-regulated after white spot syndrome virus (WSSV) infection. Silencing of LvNKRF significantly decreased the mortalities of shrimp caused by WSSV infection and down-regulated the WSSV copies and the expression of WSSV structural gene in tissues. These suggested that LvNKRF could facilitate the infection of shrimp by WSSV, which may be an additional strategy for WSSV to hijack the host NF-κB pathway to favor its own replication. The current study could provide a valuable context for further investigating the evolutionary derivation of NKRFs and facilitate the study of regulatory mechanisms of invertebrate NF-κB pathways.

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.

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.

Shrimp TAB1 interacts with TAK1 and p38 and activates the host innate immune response to bacterial infection

Mammalian TAB1 has been previously identified as transforming growth factor-β (TGF-β)-activated kinase 1 (TAK1) binding protein, which functions as the activator of TAK1 and p38. This report, for the first time, identified and characterized the homolog of TAB1 in shrimp, to be specific, the homolog gene from Litopenaeus vannamei, containing a 1560-bp open reading frame (ORF) that encoded a putative protein of 519 amino acids with the conserved PP2Cc (Serine/threonine phosphatases, family 2C, catalytic) domain in N-terminal and a TAK1 binding motif in C-terminus, has been cloned and named LvTAB1. LvTAB1 was most abundant in gills and its expression could respond significantly to a series of stimuli, including LPS, Vibrio parahemolyticus and Staphylococcus aureus. Moreover, Co-immunoprecipitation (Co-IP) experiments showed that LvTAB1 could combine with LvTAK1 as well as Lvp38, two members of IMD-NF-κB/MAPK pathway, which meant LvTAB1 could have a role in regulating the activities of these kinases. Over-expression of LvTAB1 in drosophila S2 cells could improve the transcriptional levels of antimicrobial peptide genes (AMPs) such as Diptericin (Dpt), the hallmark of drosophila NF-κB activated genes, indicating its activation effect on NF-κB pathway. Furthermore, suppression of LvTAB1 expression in vivo by RNA-interference increased the sensibility of shrimps to V. parahaemolyticus infection, implying its protective role against bacterial infection. In conclusion, these results provide some insight into the function of LvTAB1 during bacterial infection.

Transcriptomic information from Pacific white shrimp (Litopenaeus vannamei) ovary and eyestalk, and expression patterns for genes putatively involved in the reproductive process

The increased use of massive sequencing technologies has enabled the identification of several genes known to be involved in different mechanisms associated with reproduction that so far have only been studied in vertebrates and other model invertebrate species. In order to further investigate the genes involved in Litopenaeus vannamei reproduction, cDNA and SSH libraries derived from female eyestalk and gonad were produced, allowing the identification of expressed sequences tags (ESTs) that potentially have a role in the regulation of gonadal maturation. In the present study, different transcripts involved in reproduction were identified and a number of them were characterized as full-length. These transcripts were evaluated in males and females in order to establish their tissue expression profiles during developmental stages (juvenile, subadult and adult), and in the case of females, their possible association with gonad maturation was assessed through expression analysis of vitellogenin. The results indicated that the expression of vitellogenin receptor (vtgr) and minichromosome maintenance (mcm) family members in the female gonad suggest an important role during previtellogenesis. Additionally, the expression profiles of genes such as famet, igfbp and gpcr in brain tissues suggest an interaction between the insulin/insulin-like growth factor signaling pathway (IIS) and methyl farnesoate (MF) biosynthesis for control of reproduction. Furthermore, the specific expression pattern of farnesoic acid O-methyltransferase suggests that final synthesis of MF is carried out in different target tissues, where it is regulated by esterase enzymes under a tissue-specific hormonal control. Finally, the presence of a vertebrate type steroid receptor in hepatopancreas and intestine besides being highly expressed in female gonads, suggest a role of that receptor during sexual maturation.

Identification and functional analysis of a TEP gene from a crustacean reveals its transcriptional regulation mediated by NF-κB and JNK pathways and its broad protective roles against multiple pathogens

Thioester-containing proteins (TEPs) are present in a wide range of species from deuterostomes to protostomes and are thought to be involved in innate immunity. In the current study, a TEP gene homologous to insect TEPs (iTEP) from the crustacean Litopenaeus vannamei, named LvTEP1, is cloned and functionally characterized. The open reading frame (ORF) of LvTEP1 is 4383 bp in length, encoding a polypeptide of 1460 amino acids with a calculated molecular weight of 161.1 kDa LvTEP1, which is most similar to other TEPs from insects, contains some conserved sequence features, including a N-terminal signal peptide, a canonical thioester (TE) motif, and a C-terminal distinctive cysteine signature. LvTEP1 is expressed in most immune-related tissues, such as intestine, epithelium, and hemocytes, and the mRNA level of LvTEP1 is upregulated in hemocytes after bacterial and viral challenges, indicating its involvement in the shrimp innate immune response. An expression assay in Drosophila S2 cells shows LvTEP1 to be a full-length secretory protein, and processed forms are present in the supernatant. Of note, only the processed form of LvTEP1 protein can bind to both the gram-negative bacterium Vibrio parahaemolyticus and the gram-positive bacterium Staphylococcus aureus in vitro, and its abundance can be induced after bacterial treatment. Moreover, knockdown of LvTEP1 renders shrimps more susceptible to both V. parahaemolyticus and S. aureus, as well as white spot syndrome virus (WSSV) infection, suggesting its essential defensive role against these invading microbes. We also observe that the expression of LvTEP1 is regulated in a manner dependent on both NF-κB and AP-1 transcription factors in naive shrimps and in vitro, suggesting that LvTEP1 could be poised in the body cavity prior to infection and thus play an important role in basal immunity. Taken together, our findings provide some in vitro and in vivo evidence for the involvement of LvTEP1 in shrimp innate immunity and provide some insight into its expression regulation mediated by multiple transcription factors or signaling pathways.

Identification of two p53 isoforms from Litopenaeus vannamei and their interaction with NF-κB to induce distinct immune response

p53 is a transcription factor with capability of regulating diverse NF-κB dependent biological progresses such as inflammation and host defense, but the actual mechanism remains unrevealed. Herein, we firstly identified two novel alternatively spliced isoforms of p53 from Litopenaeus vannamei (LvΔNp53 and the full-length of p53, LvFLp53). We then established that the two p53 isoforms exerted opposite effects on regulating NF-κB induced antimicrobial peptides (AMPs) and white spot syndrome virus (WSSV) immediate-early (IE) genes expression, suggesting there could be a crosstalk between p53 and NF-κB pathways. Of note, both of the two p53 isoforms could interact directly with LvDorsal, a shrimp homolog of NF-κB. In addition, the activation of NF-κB mediated by LvDorsal was provoked by LvΔNp53 but suppressed by LvFLp53, and the increased NF-κB activity conferred by LvΔNp53 can be attenuated by LvFLp53. Furthermore, silencing of LvFLp53 in shrimp caused higher mortalities and virus loads under WSSV infection, whereas LvΔNp53-knockdown shrimps exhibited an opposed RNAi phenotype. Taken together, these findings present here provided some novel insight into different roles of shrimp p53 isoforms in immune response, and some information for us to understand the regulatory crosstalk between p53 pathway and NF-κB pathway in invertebrates.

Convergent Evolution of the Osmoregulation System in Decapod Shrimps

In adaptating to different aquatic environments, seawater (SW) and freshwater (FW) shrimps have exploited different adaptation strategies, which should generate clusters of genes with different adaptive features. However, little is known about the genetic basis of these physiological adaptations. Thus, in this study, we performed comparative transcriptomics and adaptive evolution analyses on SW and FW shrimps and found that convergent evolution may have happened on osmoregulation system of shrimps. We identified 275 and 234 positively selected genes in SW and FW shrimps, respectively, which enriched in the functions of ion-binding and membrane-bounded organelles. Among them, five (CaCC, BEST2, GPDH, NKA, and Integrin) and four (RasGAP, RhoGDI, CNK3, and ODC) osmoregulation-related genes were detected in SW and FW shrimps, respectively. All five genes in SW shrimps have been reported to have positive effects on ion transportation, whereas RasGAP and RhoGDI in FW shrimps are associated with negative control of ion transportation, and CNK3 and ODC play central roles in cation homeostasis. Besides, the phylogenetic tree reconstructed from the positively selected sites separated the SW and FW shrimps into two groups. Distinct subsets of parallel substitutions also have been found in these osmoregulation-related genes in SW and FW shrimps. Therefore, our results suggest that distinct convergent evolution may have occurred in the osmoregulation systems of SW and FW shrimps. Furthermore, positive selection of osmoregulation-related genes may be beneficial for the regulation of water and salt balance in decapod shrimps.

Transcriptome analysis of mud crab (Scylla paramamosain) gills in response to Mud crab reovirus (MCRV)

Mud crab (Scylla paramamosain) is an economically important marine cultured species in China's coastal area. Mud crab reovirus (MCRV) is the most important pathogen of mud crab, resulting in large economic losses in crab farming. In this paper, next-generation sequencing technology and bioinformatics analysis are used to study transcriptome differences between MCRV-infected mud crab and normal control. A total of 104.3 million clean reads were obtained, including 52.7 million and 51.6 million clean reads from MCRV-infected (CA) and controlled (HA) mud crabs respectively. 81,901, 70,059 and 67,279 unigenes were gained respectively from HA reads, CA reads and HA&CA reads. A total of 32,547 unigenes from HA&CA reads called All-Unigenes were matched to at least one database among Nr, Nt, Swiss-prot, COG, GO and KEGG databases. Among these, 13,039, 20,260 and 11,866 unigenes belonged to the 3, 258 and 25 categories of GO, KEGG pathway, and COG databases, respectively. Solexa/Illumina's DGE platform was also used, and about 13,856 differentially expressed genes (DEGs), including 4444 significantly upregulated and 9412 downregulated DEGs were detected in diseased crabs compared with the control. KEGG pathway analysis revealed that DEGs were obviously enriched in the pathways related to different diseases or infections. This transcriptome analysis provided valuable information on gene functions associated with the response to MCRV in mud crab, as well as detail information for identifying novel genes in the absence of the mud crab genome database.

Analysis of digital gene expression profiling in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress

Accumulation of nitrite in water is highly toxic to aquatic animals. To understand immune responses in shrimp under such environmental stress, a digital gene expression (DGE) technology was applied to detect the gene expression profile of the Litopenaeus vannamei hemocytes in response to nitrite for 48 h. A total of 1922 differently expressed unigenes were generated. Of these transcripts, 1269 and 653 genes were up- or down-regulated respectively. Functional categorization and pathways of the differentially expressed genes revealed that immune defense, xenobiotics biodegradation and metabolism, amino acid and nucleobase metabolic process, apoptosis were the differentially regulated processes occurring during nitrite stress. We selected 19 differential expression transcripts (DETs) to validate the sequencing results by real time quantitative PCR (qPCR). The Pearson's correlation coefficient (R) of the 19 DETs was 0.843, which confirmed the consistency and accuracy between these two approaches. Subsequently, we screened 10 genes to examine the changes in the time course of gene expression in more detail. The results indicated that expressions of ATP-binding cassette transporter (ABC transporter), caspase10, QM protein, C type lectin 4 (CTL4), protein disulfide isomerase (PDI), serine protease inhibitor 8 (SPI8), transglutaminase (TGase), chitinase1, inhibitors of apoptosis proteins (IAP) and cytochrome P450 enzyme (CYP450) were induced to participate in the anti-stress defense against nitrite. These results will provide a reference for follow-up study of molecular toxicology and valuable gene information for better understanding of immune response in L. vannamei under environmental stress.

Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001) and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001). The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences). This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species.

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.

Molecular cloning, characterization and expression analysis of Wnt4, Wnt5, Wnt6, Wnt7, Wnt10 and Wnt16 from Litopenaeus vannamei

The Wnt (Wg-type MMTV integration site) signaling represents as the negative regulator of virus-induced innate immune responses. Wnt genes act as ligands to activate the Wnt signaling. To know more about the information of Wnt genes in invertebrates, Litopenaeus vannamei Wnt genes (LvWnts) were identified and characterized. In this study, Six Wnt genes (LvWnt4, LvWnt5, LvWnt6, LvWnt7, LvWnt10 and LvWnt16) were obtained in L. vannamei. The complete cDNAs open reading frames (ORF) of LvWnt4, LvWnt5, LvWnt6, LvWnt7, LvWnt10 and LvWnt16 were 1077 bp, 1107 bp, 1350 bp, 1047 bp, 1509 bp and 1158 bp (GenBank accession no. KU169896, KU169897, KU169898, KU169899, KU169900 and KU169901), encoding 358, 368, 449, 348, 502 and 385 amino acid (aa) residues respectively. All the six members of LvWnts contain a Wnt1 domain, which is considered as an important feature of Wnt gene family. ClustalW analysis with amino acid sequences revealed that the proportion of identity with other species was more than 48% for all the LvWnts except LvWnt10 (36-41%). The phylogenetic relationship analysis illustrated that different subtype of Wnts formed their own separate branches and were placed in branch of invertebrates respectively with strong bootstrap support. The constitutive expressions of LvWnts were confirmed by RT-PCR in all the examined five developmental stages and eleven tissues of L. vannamei with different express patterns. LvWnt4, LvWnt5 and LvWnt10 were expressed highest in nerve while LvWnt6, LvWnt7 and LvWnt16 were expressed highest in intestine, stomach and gill, respectively. In addition, all the LvWnts were regulated by white spot syndrome virus (WSSV) challenges at different levels in hepatopancreas, gill and hemocytes, suggesting that Wnt genes may play a role in the defense against pathogenic virus infection in innate immune of L. vannamei.

Cloning, identification and functional analysis of a β-catenin homologue from Pacific white shrimp, Litopenaeus vannamei

Wnt signaling is known to control multiple of cellular processes such as cell differentiation, communication, apoptosis and proliferation, and is also reported to play a role during microbial infection. β-catenin is a key regulator of the Wnt signaling cascade. In the present study, we cloned and identified a β-catenin homologue from Litopenaeus vannamei termed Lvβ-catenin. The full-length of Lvβ-catenin transcript was 2797 bp in length within a 2451 bp open reading frame (ORF) that encoded a protein of 816 amino acids. Lvβ-catenin protein was comprised of several characteristic domains such as an N-terminal region of GSK-β consensus phosphorylation site and Coed coil section, a central region of 12 continuous Armadillo/β-Catenin-like repeat (ARM) domains and a C-terminal region. Real-time PCR showed Lvβ-catenin expression was responsive to Vibrio parahaemolyticus and white spot syndrome virus (WSSV) infection. Dual-reporter analysis showed that over-expression of Lvβ-catenin could induce activation of the promoter activities of several antimicrobial peptides (AMPs) such as shrimp PEN4, suggesting that Lvβ-catenin could play a role in regulating the production of AMPs. Knockdown of Lvβ-catenin enhanced the sensitivity of shrimps to V. parahaemolyticus and WSSV challenge, suggesting Lvβ-catenin could play a positive role against bacterial and viral pathogens. In summary, the results presented in this study provided some insights into the function of Wnt/β-catenin of shrimp in regulating AMPs and the host defense against invading pathogens.

Similarities between decapod and insect neuropeptidomes

Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone), a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides that have been deorphanized in insects. This includes the androgenic insulin-like peptide that seems to be homologous to drosophila insulin-like peptide 8.

Crustacean hematopoiesis

Crustacean hemocytes are important mediators of immune reactions, and the regulation of hemocyte homeostasis is of utmost importance for the health of these animals. This review discusses the current knowledge on the lineages, synthesis and differentiation of hemocytes in crustaceans. Hematopoietic tissues, their origins, and the regulation of hematopoiesis during molting, seasonal variation and infection are discussed. Furthermore, studies concerning the molecular regulation of hemocyte formation in crustaceans are also described, and the different lineages and their molecular markers are discussed and compared with several insect species. Signaling pathways and the regulation of hematopoiesis by transcription factors are typically conserved among these arthropods, whereas cytokines and growth factors are more variable and species specific. However, considering the great diversity among the crustaceans, one should be cautious in drawing general conclusions from studies of only a few species.

Allatostatins C, double C and triple C, the result of a local gene triplication in an ancestral arthropod

Allatostatin C is the arthropod homolog of vertebrate somatostatin. The gene went through a local gene triplification leading to the existence of three genes coding such peptides, allatostatins C, CC and CCC. All three genes are still present in several chelicerates, such as the horseshoe crab Limulus polyphemus, several spiders and the scorpion Mesobuthus martensii, the myriapod Strigamia maritima, as well as at least two insect species, Locusta migratoria and Athalia rosae, a sawfly. All three peptides have well conserved primary structures and peptides can easily be classified as either allatostatin C, CC or CCC. In most insect species only two of the genes have been preserved. In many species, these are CC and CCC, but in Diptera, Lepidoptera and Coleoptera it are allatostatins C and CC that are still present. In some arthropod species two or even all three genes can still be found closely associated in the genome and are present on the same scaffold showing that a local amplification was at the origin of these genes.

Transcriptome Analysis for Identification of Genes Related to Gonad Differentiation, Growth, Immune Response and Marker Discovery in The Turbot (Scophthalmus maximus)

Background

Turbot Scophthalmus maximus is an economically important species extensively aquacultured in China. The genetic selection program is necessary and urgent for the sustainable development of this industry, requiring more and more genome background knowledge. Transcriptome sequencing is an excellent alternative way to identify transcripts involved in specific biological processes and exploit a considerable quantity of molecular makers when no genome sequences are available. In this study, a comprehensive transcript dataset for major tissues of S. maximus was produced on basis of an Illumina platform.

Results

Total RNA was isolated from liver, spleen, kidney, cerebrum, gonad (testis and ovary) and muscle. Equal quantities of RNA from each type of tissues were pooled to construct two cDNA libraries (male and female). Using the Illumina paired-end sequencing technology, nearly 44.22 million clean reads in length of 100 bp were generated and then assembled into 106,643 contigs, of which 71,107 were named unigenes with an average length of 892 bp after the elimination of redundancies. Of these, 24,052 unigenes (33.83% of the total) were successfully annotated. GO, KEGG pathway mapping and COG analysis were performed to predict potential genes and their functions. Based on our sequence analysis and published documents, many candidate genes with fundamental roles in sex determination and gonad differentiation (dmrt1), growth (ghrh, myf5, prl/prlr) and immune response (TLR1/TLR21/TLR22, IL-15/IL-34), were identified for the first time in this species. In addition, a large number of credible genetic markers, including 21,192 SSRs and 8,642 SNPs, were identified in the present dataset.

Conclusion

This informative transcriptome provides valuable new data to increase genomic resources of Scophthalmus maximus. The future studies of corresponding gene functions will be very useful for the management of reproduction, growth and disease control in turbot aquaculture breeding programs. The molecular markers identified in this database will aid in genetic linkage analyses, mapping of quantitative trait loci, and acceleration of marker assisted selection programs.

Analysis of Saprolegnia parasitica Transcriptome following Treatment with Copper Sulfate

Background

Massive infection caused by oomycete fungus Saprolegnia parasitica is detrimental to freshwater fish. Recently, we showed that copper sulfate demonstrated good efficacy for controlling S. parasitica infection in grass carp. In this study, we investigated the mechanism of inhibition of S. parasitica growth by copper sulfate by analyzing the transcriptome of copper sulfate—treated S. parasitica. To examine the mechanism of copper sulfate inhibiting S. parasitica, we utilized RNA-seq technology to compare differential gene expression in S. parasitica treated with or without copper sulfate.

Results

The total mapped rates of the reads with the reference genome were 90.50% in the control group and 73.50% in the experimental group. In the control group, annotated splice junctions, partial novel splice junctions and complete novel splice junctions were about 83%, 3% and 14%, respectively. In the treatment group, the corresponding values were about 75%, 6% and 19%. Following copper sulfate treatment, a total 310 genes were markedly upregulated and 556 genes were markedly downregulated in S. parasitica. Material metabolism related GO terms including cofactor binding (33 genes), 1,3-beta-D-glucan synthase complex (4 genes), carboxylic acid metabolic process (40 genes) were the most significantly enriched. KEGG pathway analysis also determined that the metabolism-related biological pathways were significantly enriched, including the metabolic pathways (98 genes), biosynthesis of secondary metabolites pathways (42 genes), fatty acid metabolism (13 genes), phenylalanine metabolism (7 genes), starch and sucrose metabolism pathway (12 genes). The qRT-PCR results were largely consistent with the RNA-Seq results.

Conclusion

Our results indicate that copper sulfate inhibits S. parasitica growth by affecting multiple biological functions, including protein synthesis, energy biogenesis, and metabolism.

A transcriptome study on Macrobrachium rosenbergii hepatopancreas experimentally challenged with white spot syndrome virus (WSSV)

The world production of shrimp such as the Malaysian giant freshwater prawn, Macrobrachium rosenbergii is seriously affected by the white spot syndrome virus (WSSV). There is an urgent need to understand the host pathogen interaction between M. rosenbergii and WSSV which will be able to provide a solution in controlling the spread of this infectious disease and lastly save the aquaculture industry. Now, using Next Generation Sequencing (NGS), we will be able to capture the response of the M. rosenbergii to the pathogen and have a better understanding of the host defence mechanism. Two cDNA libraries, one of WSSV-challenged M. rosenbergii and a normal control one, were sequenced using the Illumina HiSeq™ 2000 platform. After de novo assembly and clustering of the unigenes from both libraries, 63,584 standard unigenes were generated with a mean size of 698bp and an N50 of 1137bp. We successfully annotated 35.31% of all unigenes by using BLASTX program (E-value <10-5) against NCBI non-redundant (Nr), Swiss-Prot, Kyoto Encyclopedia of Genes and Genome pathway (KEGG) and Orthologous Groups of proteins (COG) databases. Gene Ontology (GO) assessment was conducted using BLAST2GO software. Differentially expressed genes (DEGs) by using the FPKM method showed 8443 host genes were significantly up-regulated whereas 5973 genes were significantly down-regulated. The differentially expressed immune related genes were grouped into 15 animal immune functions. The present study showed that WSSV infection has a significant impact on the transcriptome profile of M. rosenbergii's hepatopancreas, and further enhanced the knowledge of this host-virus interaction. Furthermore, the high number of transcripts generated in this study will provide a platform for future genomic research on freshwater prawns.