Transcriptome analysis of Ruditapes philippinarum hepatopancreas provides insights into immune signaling pathways under Vibrio anguillarum infection

A haplotype-like, chromosome-level assembled and annotated genome of Biomphalaria glabrata, an important intermediate host of schistosomiasis and the best studied model of schistosomiasis vector snails

Schistosomiasis is one of the world's most devastating parasitic diseases, afflicting 251 million people globally. The Neotropical snail Biomphalaria glabrata is an important intermediate host of the human blood fluke Schistosoma mansoni and a predominant model for schistosomiasis research. To fully exploit this model snail for biomedical research, here we report a haplotype-like, chromosome-level assembled and annotated genome of the homozygous iM line of B. glabrata that we developed at the University of New Mexico. Using multiple sequencing platforms, including Illumina, PacBio, and Omni-C sequencing, 18 sequence contact matrices representing 18 haploid chromosomes (2n = 36) were generated (337x genome coverage), and 96.5% of the scaffold sequences were anchored to the 18 chromosomes. Protein-coding genes (n = 34,559), non-coding RNAs (n = 2,406), and repetitive elements (42.52% of the genome) were predicted for the whole genome, and detailed annotations for individual chromosomes were also provided. Using this genomic resource, we have investigated the genomic structure and organization of the Toll-like receptor (TLR) and fibrinogen-domain containing protein (FReD) genes, the two important immune-related gene families. Notably, TLR-like genes are scattered on 13 chromosomes. In contrast, almost all (39 of 40) fibrinogen-related genes (FREPs) (immunoglobulin superfamily (IgSF) + fibrinogen (FBG)) are clustered within a 5-million nucleotide region on chromosome 13, yielding insight into mechanisms involved in the diversification of FREPs. This is the first genome of schistosomiasis vector snails that has been assembled at the chromosome level, annotated, and analyzed. It serves as a valuable resource for a deeper understanding of the biology of vector snails, especially Biomphalaria snails.

Genome-Wide Identification and Characterization of MITF Genes in Ruditapes philippinarum and Their Involvement in the Immune Response to Vibrio anguillarum Infection

Studies have shown that the shellfish have innate immune system, which is a very important immune form of shellfish, and they rely on the innate immune system to resist diseases. As a transcription factor, Microphthalmia-associated transcription factor (MITF) plays a regulatory role in immune response and the shell color is also an important index for the breeding of excellent varieties of R. philippinarum. The research on immune response mechanism of RPMITFs can provide important reference data for the breeding of excellent clam varieties. In the genome of R. philippinarum, the RPMITF genes family of shell color-related gene family was selected as the target gene of this experiment. There are 12 RpMITF genes named RpMITF1, RpMITF2, RpMITF3, RpMITF4, RpMITF5, RpMITF6, RpMITF7, RpMITF8, RpMITF9, RpMITF10, RpMITF11, and RpMITF12. The open reading frame length is 639, 1233, 996, 1239, 675, 624, 816, 1365, 612, 1614, 1122, and 486 bp, encoding 212, 410, 331, 412, 224, 207, 271, 454, 203, 537, 373, and 161 aa, respectively. The predicted molecular weight range of amino acids is 18.85-62.61 kda, and the isoelectric point range is 5.26-9.44. Real-time quantitative PCR was used to detect the gene expression of RpMITF gene family in hepatopancreas tissues of two populations of Manila clam at 6 time points (0, 3, 6, 12, 24, and 48 h) after Vibrio anguillarum stress. The results show that RpMITF gene family was significantly expressed in hepatopancreas of two clam populations after V. anguillarum stress (P < 0.05).

Applying genetic technologies to combat infectious diseases in aquaculture

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

Characteristic and antibacterial effect of a histone H2A and its preliminary roles in extracellular traps in manila clam Ruditapes philippinarum

In the present study, a histone H2A (designed as RpH2A) was identified and characterized from clam Ruditapes philippinarum, and its open reading frame (ORF) was of 387 bp encoding a polypeptide of 128 amino acids. The deduced amino acid sequence of RpH2A shared high identities ranging from 57.1% to 96.1% with that of other identified H2A. The mRNA expression of RpH2A was up-regulated significantly after Vibrio anguillarum challenge. The recombinant RpH2A protein (rRpH2A) displayed significantly binding affinity to lipopolysaccharide (LPS) and peptidoglycan (PGN) in vitro, and also exhibited antimicrobial properties against Escherichia coli. In addition, the antimicrobial RpH2A was shown to co-localize with extracellular traps (ETs) released from hemocytes induced by E. coli, suggesting that RpH2A might contribute to eliminate invading bacteria in clam ETs. Altogether, our data revealed that RpH2A could function as antimicrobial peptides, which might play a crucial role in the immune responses of hemocytes ETs in clams.

Molecular characterization of peptidoglycan recognition proteins from Mytilus coruscus

Mytilus shows great immune resistance to various bacteria from the living waters, indicating a complex immune recognition mechanism against various microbes. Peptidoglycan recognition proteins (PGRPs) play an important role in the defense against invading microbes via the recognition of the immunogenic substance peptidoglycan (PGN). Therefore, eight PGRPs were identified from the gill transcriptome of Mytilus coruscus. The sequence features, expression pattern in various organs and larval development stages, and microbes induced expression profiles of these Mytilus PGRPs were determined. Our data revealed the constitutive expression of PGRPs in various organs with relative higher expression level in immune-related organs. The expression of PGRPs is developmentally regulated, and most PGRPs are undetectable in larvae stages. The expression level of most PGRPs was significantly increased with in vivo microbial challenges, showing strong response to Gram-positive strain in gill and digestive gland, strong response to Gram-negative strain in hemocytes, and relative weaker response to fungus in the three tested organs. In addition, the function analysis of the representative recombinant expressed PGRP (rMcPGRP-2) confirmed the antimicrobial and agglutination activities, showing the immune-related importance of PGRP in Mytilus. Our work suggests that Mytilus PGRPs can act as pattern recognition receptors to recognize the invading microorganisms and the antimicrobial effectors during the innate immune response of Mytilus.

Integrated RNA-seq and RNAi Analysis of the Roles of the Hsp70 and SP Genes in Red-Shell Meretrix meretrix Tolerance to the Pathogen Vibrio parahaemolyticus

The "Wanlihong" Meretrix meretrix (WLH-M) clam is a new variety of this species that has a red shell and stronger Vibrio tolerance than ordinary M. meretrix (ORI-M). To investigate the molecular mechanisms responsible for the WLH-M strain's tolerance to Vibrio, we challenged clams with Vibrio parahaemolyticus and then assessed physiological indexes and conducted transcriptome analysis and RNA interference experiments. The mortality, tissue bacterial load, and hemocyte reactive oxygen species level of ORI-M were significantly higher than those of WLH-M, whereas the content and activity of lysozyme were significantly lower. Gene Ontology functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that immune and metabolic pathways were enriched in Vibrio-challenged clams. The expressions of the heat shock protein 70 (Hsp70) and serine protease (SP) genes, which are involved in antibacterial immunity, were significantly upregulated in WLH-M but not in ORI-M, while the expression of the kynurenine 3-monooxygenase gene, a proinflammatory factor, was significantly downregulated in WLH-M. RNA interference experiments confirmed that Hsp70 and SP downregulation could result in increased mortality of WLH-M. Therefore, we speculate that Hsp70 and SP may be involved in the antibacterial immunity of WLH-M in vivo. Our data provided a valuable resource for further studies of the antibacterial mechanism of WLH-M and provided a foundation for the breeding of pathogen-resistant strains.

Effects of environmental concentrations of the fragrance amyl salicylate on the mediterranean mussel Mytilus galloprovincialis

Amyl salicylate (AS) is a fragrance massively used as a personal care product and following the discharged in wastewaters may end up in the aquatic environment representing a potential threat for the ecosystem and living organisms. AS was recently detected in water of the Venice Lagoon, a vulnerable area continuously subjected to the income of anthropogenic chemicals. The lagoon is a relevant area for mollusc farming, including the Mediterranean mussels (Mytilus galloprovincialis) having an important economic and ecological role. Despite high levels of AS occurred in water of the Lagoon of Venice, no studies investigated the possible consequences of AS exposures on species inhabiting this ecosystem to date. For the first time, we applied a multidisciplinary approach to investigate the potential effects of the fragrance AS on Mediterranean mussels. To reach such a goal, bioaccumulation, cellular, biochemical, and molecular analyses (RNA-seq and microbiota characterization) were measured in mussels treated for 7 and 14 days with different AS Venice lagoon environmental levels (0.1 and 0.5 μg L^-1). Despite chemical investigations suggested low AS bioaccumulation capability, cellular and molecular analyses highlighted the disruption of several key cellular processes after the prolonged exposures to the high AS concentration. Among them, potential immunotoxicity and changes in transcriptional regulation of pathways involved in energy metabolism, stress response, apoptosis and cell death regulations have been observed. Conversely, exposure to the low AS concentration demonstrated weak transcriptional changes and transient increased representation of opportunistic pathogens, as Arcobacter genus and Vibrio aestuarianus. Summarizing, this study provides the first overview on the effects of AS on one of the most widely farmed mollusk species.

Molecular Mechanisms Underlying Vibrio Tolerance in Ruditapes philippinarum Revealed by Comparative Transcriptome Profiling

The clam Ruditapes philippinarum is an important species in the marine aquaculture industry in China. However, in recent years, the aquaculture of R. philippinarum has been negatively impacted by various bacterial pathogens. In this study, the transcriptome libraries of R. philippinarum showing different levels of resistance to challenge with Vibrio anguillarum were constructed and RNA-seq was performed using the Illumina sequencing platform. Host immune factors were identified that responded to V. anguillarum infection, including C-type lectin domain, glutathione S-transferase 9, lysozyme, methyltransferase FkbM domain, heat shock 70 kDa protein, Ras-like GTP-binding protein RHO, C1q, F-box and BTB/POZ domain protein zf-C2H2. Ten genes were selected and verified by RT-qPCR, and nine of the gene expression results were consistent with those of RNA-seq. The lectin gene in the phagosome pathway was expressed at a significantly higher level after V. anguillarum infection, which might indicate the role of lectin in the immune response to V. anguillarum. Comparing the results from R. philippinarum resistant and nonresistant to V. anguillarum increases our understanding of the resistant genes and key pathways related to Vibrio challenge in this species. The results obtained here provide a reference for future immunological research focusing on the response of R. philippinarum to V. anguillarum infection.

Transcriptome-wide identification and characterization of toll-like receptors response to Vibrio anguillarum infection in Manila clam (Ruditapes philippinarum)

The Manila clam (Ruditapes philippinarum), one of the major marine aquaculture species in China, is susceptible to infection with the pathogen Vibrio, which results in massive mortality and economic losses. Toll-like receptors (TLRs) are significant pattern recognition receptors (PRRs) of innate immunity that are involved in immune regulation against pathogenic invasion. Molecular characterization of Manila clam TLRs and investigations of their immune functions are essential to prevent and control Vibrio infection. In the present research, eight cDNA sequences of R. philippinarum TLRs (RpTLRs) were identified from previous transcriptome libraries and then classified into four groups, namely, P-TLR (one sequence), V-TLR (one sequence), Ls-TLR (two sequences) and sP-TLR (four sequences), based on the corresponding LRR domain arrangement of their protein structures within the typical TLR motifs. A selective pressure test firstly suggested that the molluscan P-TLR, V-TLR, Ls-TLR and sP-TLR families underwent positive selection, and different numbers of positive selection sites (PSSs) were identified in different domains of the four types of RpTLRs, as determined by PAML and analysis of website data. These findings indicated that the evolution of RpTLRs may be associated with their immune recognition and function. Furthermore, tissue-specific expression analysis showed that all RpTLRs were ubiquitously expressed in all test tissues and were dominant in hemocytes. Quantitative real-time PCR revealed that the cDNA expression of all eight RpTLRs was upregulated after injection with Vibrio anguillarum (P < 0.01) in R. philippinarum hemocytes, revealing that these RpTLRs play important roles in responding to pathogenic stimulation. In summary, these findings provide a foundation for future investigations of the molecular classification and evolutionary patterns of Toll-like receptors in invertebrates, and the innate immune responses of TLR signaling pathways in Mollusca.

Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Simple Summary

Riptortus pedestris is a widely distributed pest insect in East Asia that causes considerable economic losses. In this study, we applied the Illumina HiSeq6000 platform to construct and sequence the transcriptome libraries of R. pedestris during all life stages. First, a total of 60,058 unigenes were assembled from raw data, and then annotated and classified with various databases. Furthermore, different numbers of differentially expressed genes were calculated by pairwise comparisons of all life stages, and some of these DEGs were associated with various functions by GO and KEGG analysis. Additionally, a total number of 35,158 SSRs and 715,604 SNPs were identified from all the transcriptome libraries. Finally, we analyzed ten wing formation-related signaling pathways, and detected the molecular and expression characterization of five wing development-related genes by qRT-PCR for all developmental stages of R. pedestris. Collectively, all these data may pave the avenue for exploring the developmental processes of hemimetabolous insects and pest management.

Abstract

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

Genome-wide identification and expression profiling of TYR gene family in Ruditapes philippinarum under the challenge of Vibrio anguillarum

Tyrosinase (EC1.14.18.1, TYR) is also called phenol oxidase, is not only involved in pigmentation but also plays an important role in modulating innate immunity in invertebrates. Tyrosinase is a copper containing metalloenzyme. The tyrosinase protein has two copper binding sites and three conserved histidines. In this study, 21 tyrosinase genes (RpTYR) were obtained from the whole genome of Ruditapes philippinarum. Their open reading frames were from 951 to 5424 aa, the range of predicted relative molecular weight from 36.72 to 203.81 kDa, and the range of isoelectric point from 4.72 to 9.88. Transcriptome analysis showed that RpTYR gene was expressed specifically in different developmental stages, adult tissues, four strains and two groups with different shell colors. Besides, the expression profiles of 21 RpTYRs were investigated against the immune response of R. philippinarum to a Vibrio challenge. The qPCR results showed that RpTYRs were involved in the immune response of R. philippinarum after Vibrio anguillarum challenge. This study provides preliminary evidence that the tyrosinases genes are involved in the immune defense and the potential immune function of R. philippinarum. Overall, these findings suggested that the expansion of TYR genes may play vital roles in larval development, the formation of shell color pattern, and immune response in R. philippinarum.

Transcriptomic analysis of Manila clam Ruditapes philippinarum under lipopolysaccharide challenge provides molecular insights into immune response

The Manila clam, Ruditapes philippinarum, is an economically important shellfish in marine aquaculture. A better understanding of the immune system in R. philippinarum will provide the basis for the development of strategies to mitigate the impact of infectious diseases affecting this species but can also be of relevance for other bivalves of commercial interest. In this study, the transcriptional response of the Manila clam under lipopolysaccharide (LPS) challenge was characterized using RNA sequencing. The transcriptomes of LPS challenged group of clams (LH1, LH2 and LH3), and the PBS control group (CH1, CH2 and CH3), were sequenced with the Illumina HiSeq platform. Compared with the unigene expression profile of the control group, 223 unigenes were up-regulated and 389 unigenes were down-regulated in the LPS challenged group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that signal transduction, defense response, and immune-related pathways such as Chemokine signaling pathway, Complement and coagulation cascades, NOD-like receptor signaling pathway, and Inflammatory mediator regulation of TRP channels in sensory system were the most highly enriched pathways among the genes that were differentially expressed under LPS challenge. This study present understanding of the molecular basis underpinning response to LPS challenge and provides useful information for future work on the molecular mechanism of pathogen resistance and immunity in Manila clam.

New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)

Background

Manila clam (Ruditapes philippinarum) is a worldwide commercially important marine bivalve species. In recent years, however, microbial diseases caused high economic losses and have received increasing attention. To understand the molecular basis of the immune response to pathogen-associated molecular patterns (PAMPs) in R. philippinarum, transcriptome libraries of clam hepatopancreas were constructed at 24 h post-injection with Lipopolysaccharide (LPS), peptidoglycan (PGN), and polyinosinic-polycytidylic acid (poly(I:C)) and phosphate-buffered saline (PBS) control by using RNA sequencing technology (RNA-seq).

Results

A total of 832, 839, and 188 differentially expressed genes (DEGs) were found in LPS, PGN, and poly(I:C) challenge group compared with PBS control, respectively. Several immune-related genes and pathways were activated in response to the different PAMPs, suggesting these genes and pathways might specifically participate in the immune response to pathogens. Besides, the analyses provided useful complementary data to compare different PAMPs challenges in vivo. Functional enrichment analysis of DEGs demonstrated that PAMPs responsive signal pathways were related to apoptosis, signal transduction, immune system, and signaling molecules and interaction. Several shared or specific DEGs response to different PAMPs were revealed in R. philippinarum, including pattern recognition receptors (PRRs), antimicrobial peptides (AMPs), interferon-induced proteins (IFI), and some other immune-related genes were found in the present work.

Conclusions

This is the first study employing high throughput transcriptomic sequencing to provide valuable genomic resources and investigate Manila clam response to different PAMPs through in vivo challenges with LPS, PGN, and poly(I:C). The results obtained here provide new insights to understanding the immune characteristics of R. philippinarum response to different PAMPs. This information is critical to elucidate the molecular basis of R. philippinarum response to different pathogens invasion, which potentially can be used to develop effective control strategies for different pathogens.

Transcriptome analysis of Catarina scallop (Argopecten ventricosus) juveniles treated with highly-diluted immunomodulatory compounds reveals activation of non-self-recognition system

Marine bivalve hatchery productivity is continuously challenged by apparition and propagation of new diseases, mainly those related to vibriosis. Disinfectants and antibiotics are frequently overused to prevent pathogen presence, generating a potential negative impact on the environment. Recently, the use of highly diluted compounds with immunostimulant properties in marine organisms has been trailed successfully to activate the self-protection mechanisms of marine bivalves. Despite their potential as immunostimulants, little is known about their way of action. To understand their effect, a comparative transcriptomic analysis was performed with Argopecten ventricosus juveniles. The experimental design consisted of four treatments formulated from pathogenic Vibrio lysates at two dilutions: [(T1) Vibrio parahaemolyticus and Vibrio alginolyticus 1D; (T2) V. parahaemolyticus and V. alginolyticus 7C]; minerals [(T3) PhA+SiT 7C], scorpion venom [(T4) ViT 31C]; and one control (C1) hydro-alcoholic solution (ethanol 1%). The RNA sequencing (RNAseq) analysis showed a higher modulation of differentially expressed genes (DEG) in mantle tissue compared to gill tissue. The scallops that showed a higher number of DEG related to immune response in mantle tissue corresponded to T1 (V. parahaemolyticus and V. alginolyticus lysate) and T3 (Silicea terra® - Phosphoric acid®). The transcriptome analysis allowed understanding some interactions between A. ventricosus juveniles and highly-diluted treatments.

Molecular and expression characterization of Toll-like receptor family genes from the Anadara sativa (Bivalvia, Arcidae) transcriptome

Innate immunity plays an important role in invertebrates because it provides the first line of protection by recognizing invading microbial pathogens and then activating downstream signaling pathways. However, until now, increasing reports of clam diseases did not include those of Anadara sativa, which are widely distributed and economically important maritime clams. In the present study, transcriptome libraries of untreated (termed H) and Vibrio anguillarum-challenged (termed HV) A. sativa hepatopancreases were constructed and sequenced using the Illumina HiSeq4000 platform. In total, we obtained 78,012,510 and 84,937,516 clean reads from 80,006,030 to 86,871,742 raw data reads, respectively, assembled by different software programs. Furthermore, 150,274 unigenes were generated from 196,003 transcripts, with an N50 length of 1088 bp, and then annotated with the SwissProt, NR, NT, PFAM, KO, GO, KOG and KEGG databases. Moreover, 3982 differentially expressed unigenes (H vs HV) were determined, with 3583 upregulated and 399 downregulated genes. Among these differentially expressed unigenes, 207 unigenes were found using KEGG annotation in 16 immune-related signaling pathways, such as Toll-like receptor (TLR), NOD-like receptor (NLR), and RIG-I-like receptor (RLR) signaling pathways. Finally, we selected 11 full-length TLRs and classified them into 3 groups, namely, one V-TLR, four Ls-TLR and six sP-TLR; furthermore, we validated the increased expression patterns of the 11 TLRs in response to LPS injection. In summary, these results revealed multiple findings on potential immune-related genes, such as the differential expression analysis and annotation based on the A. sativa transcriptome in response to V. anguillarum stimulation, and explored the molecular and expression characterization of A. sativa TLRs, which provide new insights into the innate immune responses and defense mechanisms in shellfish.

Dynamic immune and metabolism response of clam Meretrix petechialis to Vibrio challenge revealed by a time series of transcriptome analysis

Meretrix petechialis is an important commercial aquaculture species in China. During the clam culture period, mass mortality events often occurred due to the Vibrio infection. In this paper, M. petechialis were challenged with Vibrio parahaemolyticus immersion to simulate a natural infection, and the infection process were divided into four phases including latency, prodrome, onset and recovery phases based on the clam mortality data. Then, the dynamic response of clams to Vibrio infection at different infection phases were investigated by transcriptome analysis. A total of 38,067 differentially expressed genes (DEGs) were identified at different infection phases. DEG annotations showed that immune-related and metabolism-related signaling pathways were enriched, indicating that immune defense and metabolism process play key roles during bacterial infection. Three kinds of expression pattern were classified by cluster analysis, including U-shape, L-shape and inverted V-shape. Anabolism and cellular growth proliferation related signaling pathways were repressed (long-lasting or transient) during bacterial infection. However, the immune related signaling pathways with different immune functions showed induction expression or repression expression against bacterial infection, which indicated that immune system take different strategies against bacterial infection. Furthermore, some signaling pathways such as PI3K-Akt signaling pathway both involved in immune defense and cell metabolism. This study provides a sight that the dynamic immunity and metabolic responses may be integrated to improve the host survival and shift more energy for immune defense.

New insight into the molecular basis of Fe (III) stress responses of Procambarus clarkii by transcriptome analysis

Iron in excess can have toxic effects on living organisms. In China, the freshwater crayfish Procambarus clarkii is a source of aquatic food with high-quality protein and has significant commercial value. P. clarkii shows oxidative stress on exposure to heavy metals, and antioxidant enzymes, such as ubiquitination enzymes and proteasomes, play important roles in oxidative stress. To understand the antioxidant defense system of P. clarkii, we analyzed the hepatopancreas transcriptomes of P. clarkii after stimulation with FeCl₃. In total, 5199 differentially expressed genes (DEGs) were identified (2747 upregulated and 2452 downregulated). GO analysis revealed that these DEGs belonged to 16 cellular component, 16 molecular function, and 19 biological process subcategories. A total of 1069 DEGs were classified into 25 categories by using COG. Some antioxidant defense pathways, such as "Ubiquitin mediated proteolysis" and "Glutathione metabolism," were identified using KEGG. In addition, quantitative real time-PCR (qRT-PCR) substantiated the up-regulation of a random selection of DEGs including antioxidant and immune defense genes. We obtained information for P. clarkii transcriptome databases and new insights into the responses of P. clarkii hepatopancreas to heavy metals.

Transcriptome analysis and discovery of genes involved in immune pathways in Solen strictus (Gould, 1861) under Vibrio anguillarum

The Solen strictus (Gould, 1861) has been recognized as an important marine economic bivalve in Eastern and Southeast Asia. To gain a better understanding of the S. strictus immune system and its related genes in response to bacterial infections, we performed a comparative gene transcription analysis from S. strictus with Vibrio anguillarum through RNA-Seq technology, meanwhile the differentially expressed genes (DEGs) were investigated. After assembly, a total of 195,774 transcripts with an average length of 996 bp were obtained. Total 153,038 unigenes were annotated in the nr, Swiss-Prot, KEGG, COG, KOG, GO and Pfam databases, and 56,597 unigenes (36.98%) were annotated in at least one database. After bacterial challenge, there were 1588 significant differentially expressed genes (DEGs) between the challenged and control groups, including 999 up-regulated and 589 down-regulated genes. All the DEGs were classified into three gene ontology categories, and allocated to 225 KEGG pathways. Immune-related genes were detected from immune system pathways among the top 20 enriched pathways, such as Toll-like receptor signaling, RIG-I-like receptor signaling and NOD-like receptor signaling pathway. In addition, 56,079 potential simple sequence repeats (SSRs) and 1,031,521 candidate single nucleotide polymorphisms (SNPs) were detected and identified in the S. strictus transcriptome. Results of the present study will provide valuable theoretical resources for future genetic and genomic research on S. strictus. The research results will be helpful for improving the efficiency and quality of artificial breeding, establishing genetic linkage map, and enhancing health management for this species.

High individual variability in the transcriptomic response of Mediterranean mussels to Vibrio reveals the involvement of myticins in tissue injury

Mediterranean mussels (Mytilus galloprovincialis) are sessile filter feeders that live in close contact with numerous marine microorganisms. As all invertebrates, they lack an adaptive immune response and how these animals are able to respond to a bacterial infection and discriminate it from their normal microbiome is difficult to understand. In this work, we conducted Illumina sequencing of the transcriptome of individual mussels before and after being infected with Vibrio splendidus. The control mussels were injected with filtered seawater. We demonstrate that a great variability exists among individual transcriptomes and that each animal showed an exclusive repertoire of genes not shared with other individuals. The regulated genes in both the control and infected mussels were also analyzed and, unexpectedly, the sampling before the injection was considered a stress stimulus strong enough to trigger and modulate the response in hemocytes, promoting cell migration and proliferation. We found a clear response against the injection of filtered seawater, suggesting a reaction against a tissue injury in which the myticins, the most expressed antimicrobial peptides in mussel, appeared significantly up regulated. Functional experiments with flow cytometry confirmed the transcriptomic results since a significant alteration of hemocyte structures and a decrease in the number of hemocytes positive for myticin C were found only after a Vibrio infection and not observed when mussels were bled before, generating a tissue injury. Therefore, we report the involvement of myticins in the response to a danger signal such as a simple injection in the adductor muscle.

Do the toll-like receptors and complement systems play equally important roles in freshwater adapted Dolly Varden char (Salvelinus malma)?

Unlike the normal anadromous lifestyle, Chinese native Dolly Varden char (Salvelinus malma) is locked in land and lives in fresh water lifetime. To explore the effect of freshwater adaption on its immune system, we constructed a pooled cDNA library of hepatopancreas and spleen of Chinese freshwater Dolly Varden char (S. malma). A total of 27,829 unigenes were generated from 31,233 high-quality transcripts and 17,670 complete open reading frames (ORF) were identified. Totally 25,809 unigenes were successfully annotated and it classified more native than adaptive immunity-associated genes, and more genes involved in toll-like receptor signal pathway than those in complement and coagulation cascades (51 vs 3), implying the relative more important role of toll-like receptors than the complement system under bacterial injection for the freshwater Dolly Varden char. These huge different numbers of TLR and complement system identified in freshwater Dolly Varden char probably caused by distinct evolution pressure patterns between fish TLR and complement system, representative by TLR3 and TLR5 as well as C4 and C6, respectively, which were under purifying and positively selecting pressure, respectively. Further seawater adaptation experiment and the comparison study with our library will no doubt be helpful to elucidate the effect of freshwater adaption of Chinese native Dolly Varden char on its immune system.

Survival, Virulent Characteristics, and Transcriptomic Analyses of the Pathogenic Vibrio anguillarum Under Starvation Stress

Many bacteria have developed strategies for metamorphosis into sophisticated survival forms to survive extended periods of environmental stress. As a global causative agent of vibriosis in marine fish farming, Vibrio anguillarum (V. anguillarum) can efficiently grow and proliferate under environmental stress, but the specific mechanism is not clear. In the present study, survival, virulent characteristics, and transcriptomic analysis of the V. anguillarum BH1 were performed under starvation stress. The results demonstrated that V. anguillarum was still culturable and showed rippled surface after 6 months of starvation. Starved cells maintained their infectivity in half-smooth tongue sole (Cynoglossus semilaevi). Detection of virulence factors and virulence-associated genes in starved cells showed that the starved strain still produced β-hemolysis on rabbit blood agar, caseinase, dnase, and gelatinase, and possessed empA, vah1, vah2, vah3, vah4, vah5, rtxA, flaA, flaD, flaE, virC, tonB, mreB, toxR, rpoS, and ftsZ virulence-related genes. In addition, we first reported the RNA-seq study for V. anguillarum with and without starvation treatment for a period of 6 months and emphasized the regulation of gene expression at the whole transcriptional level. It indicated that V. anguillarum expressed 3,089 and 3,072 genes in the control group and starvation stress group, respectively. The differently expressed genes (DEGs) of the starved strain were thereby identified, including 251 up-regulated genes and 272 down-regulated genes in comparison with the non-starved strain. Gene Ontology (GO) analysis and Kyto Encyclopedia Genes and Genomes (KEGG) enrichment analysis of DEGs were also analyzed. GO functional classification revealed that among the significantly regulated genes with known function categories, more genes affiliated with signal transducer activity, molecular transducer activity, and cell communication were significantly up-regulated, and more genes affiliated with cellular macromolecule, cellular component, and structural molecule activity were significantly down-regulated. In addition, the DEGs involved in the pathway of two-component system was significantly up-regulated, and the pathways of ribosome and flagellar assembly were significantly down-regulated. This study provides valuable insight into the survival strategies of V. anguillarum and suggests that a portion of the bacterial populations may remain pathogenic while persisting under starvation stress by up-regulating or down-regulating a series of genes.

Evolutionary and functional analysis of Cyclina sinensis c-Jun AP-1 gene in response to LPS stimulation

The transcription factor activator protein-1 (AP-1) plays an essential and critical role in the regulation of numerous downstream genes involved in various physiological and chemical responses. In this study, we identified a full-length cDNA of the c-Jun AP-1 gene (termed Csc-Jun) from the transcriptome library in Cyclina sinensis. The cDNA contains an 825-bp open reading frame that encodes a 274-amino acid protein sequence, including a characteristic Jun transcription factor domain and a highly conserved basic leucine zipper (bZIP) signature that shares 90% identity to that of Ruditapes philippinarum. Furthermore, a phylogenetic analysis using MrBayes and PhyML software (with Bayesian and maximum likelihood approaches, respectively) revealed that the c-Jun AP-1 family genes might be involved in adapting to various environments in different invertebrates. We implemented the PAML software with the maximum likelihood method to further select and verify the positive selection sites (PSSs) in the Mollusca c-Jun AP-1 genes, and we detected four PSSs located in the Jun transcription factor domain. In addition, a spatial expression analysis showed that the Csc-Jun cDNA transcript was ubiquitously expressed in all of the tested tissues and was strongly expressed in the hepatopancreas and weakly expressed in the tissues of the hemocytes, gill filaments, mantle and adductor muscle. Quantitative real-time PCR showed that the expression profiles of Csc-Jun were significantly upregulated at different times in all of the tested tissues when challenged with lipopolysaccharide (LPS). Furthermore, knockdown of Csc-Jun by RNA interference resulted in a higher mortality of C. sinensis following LPS exposure. Finally, we explored the function of the TLR13-MyD88 signaling pathway in the innate immunity of C. sinensis by RNA interference and immune challenges. The results revealed that the mRNA expression levels of Csc-Jun were all decreased (P < 0.01) in normal and stimulated C. sinensis hemocytes. These data collectively indicated that the c-Jun AP-1 gene might play vital roles in innate immunity and provide new evidence for the evolutionary patterns of innate immune genes in Mollusca.

Differential transcriptome analysis of zebrafish (Danio rerio) larvae challenged by Vibrio parahaemolyticus

Zebrafish embryo and larva represent a useful in vivo model for identification of host innate immune responses to bacterial infection. Vibrio parahaemolyticus is a typical zoonotic pathogen worldwide that causes acute gastroenteritis in humans and vibriosis in fishes. However, the mechanism of the innate immune response in the zebrafish larvae infected by V. parahaemolyticus has not been clear. We analysed the transcriptomic profile of 3 days post-fertilization (dpf) zebrafish larvae immersed in V. parahaemolyticus 13 (Vp13) strain suspension for 2 hr. A total of 602 differentially expressed genes (DEGs) were identified in the infection group, of which 175 (29.07%) genes were upregulated and 427 (70.93%) genes were downregulated. These altered genes encoded complement and coagulation cascades, chemokine, TNF signalling pathway, NF-κB signalling pathway and JAK-STAT signalling pathway. Some significant DEGs, such as mmp13, cxcr4a, ccl20, hsp70, gngt, serpina1l, il8, cofilin and il11, were subjected to quantitative gene expression analysis, and the results were consistent with those of the transcriptome profile. These results clearly demonstrated that exposure to V. parahaemolyticus for 2 hr could activate innate immune response in 3dpf larvae by altered expression of downstream signalling pathway genes of pattern recognition receptors (PRRs). Our results also provide a useful reference for future analysis of signal transduction pathways and pathogenesis mechanisms underlying the systemic innate immune response to the external bacteria of V. parahaemolyticus.

Comparative and evolutionary analysis of an adapter molecule MyD88 in invertebrate metazoans

The myeloid differentiation factor 88 (MyD88) is an essential adapter in Toll-like receptor (TLR) signalling pathways, with TLR the first pattern-recognition receptor (PRR) that was discovered in Drosophila. In the present study, a MyD88 gene was identified and characterized from a commercially important shellfish, Scapharca subcrenata, including a DEATH domain and TIR domain conserved within other molluscs. Furthermore, comparative genomic evidence revealed that MyD88 was of different lengths and contained quantitative exon and intron regions, which might be involved in specific mechanisms. To further explore the phylogenetic relationships of invertebrate metazoan MyD88, we applied MrBayes and PhyML software to construct phylogenetic trees using Bayesian and maximum likelihood approaches, respectively, which suggested that the MyD88 of Arthropoda was closely related to lower invertebrates, in contrast to morphological taxonomy. Finally, we investigated the evolutionary patterns and location of positive selection sites (PSSs) in the MyD88 gene from Arthropoda, Mollusca and Insecta using PAML software with the maximum likelihood method. The data showed that positive selection sites were detected in these groups, and partial sites were located in the TIR domain but were not found in the DEATH domain. To summarize, in this study, we report on the diversification of MyD88 in invertebrate metazoans, the specific evolutionary position of Arthropoda MyD88, and the positive selection pressures on MyD88 of Arthropoda, Mollusca and Insecta. These results are a valuable contribution to understand and clarify the evolutionary pattern of TLR/MyD88 signalling pathways in invertebrate and vertebrate taxa.

The spread of Vibrio parahaemolyticus in tissues of the Pacific white shrimp Litopenaeus vannamei analyzed by PCR and histopathology

V. parahaemolyticus are bacteria that cause the Acute Hepatopancreatic Necrosis Disease (AHPND), or Early Mortality Syndrome (EMS), in shrimp. To further understand the pathogenesis mechanisms of V. parahaemolyticus infection in shrimp, the spreading of this bacterium in various tissues was investigated. The spread of infection in shrimp that were exposed to seawater bacteria was studied by PCR and histopathology at 1 min, 1, 6, 12, 24, 48 and 72 h after exposure. The PCR results showed that V. parahaemolyticus was at its most widespread at 6 h after exposure, at which point V. parahaemolyticus was found in the gills, hepatopancreas, intestine, muscles, and hemolymph. However, examinations after 6 h of infection found only small amounts of V. parahaemolyticus in hepatopancreas and intestines. Histopathology of the hepatopancreas showed abnormalities on gross examination at 1 min-72 h after exposure. This study indicates that V. parahaemolyticus can spread quickly by using the hepatopancreas as the target tissue. After 6 h of infection, V. parahaemolyticus was eliminated by immune system while their toxins still caused damage to shrimp tissues.

Transcriptome analysis of yellow catfish (Pelteobagrus fulvidraco) liver challenged with polyriboinosinic polyribocytidylic acid (poly I:C)

Yellow catfish (Pelteobagrus fulvidraco) is one of the most important economic freshwater species in China. However, infection by bacterial pathogenic diseases has caused high mortality and great economic loss in aquaculture. It is necessary for disease control to know more about the P. fulvidraco immune system and its related genes in response to bacterial or viral infections. In this study, the transcriptomic profiles of liver from P. fulvidraco stimulated by polyriboinosinic polyribocytidylic acid (poly I:C) was analyzed using high-throughput sequencing method. After assembly and annotation, total 67,447 unigenes were acquired, with an average length of 1091 bp. Under the infection of poly I:C, 522 differentially expressed genes (DEGs) were identified, including 307 up-regulated genes and 215 down-regulated genes. To further investigate the immune-related DEGs, Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed. The result of GO enrichment indicated gene response to external stimulus, regulation of response to stimulus, cellular response to stimulus, immune response and immune system progress. Significant KEGG enrichment analysis identified major immune related pathways. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis revealed that 13 immune response genes were identified to be up-regulated after 12 h of poly I:C stimulation compared to controls. Taken together, the results of our study are beneficial for better understanding of the immune system and defense mechanisms of yellow catfish in response to poly I:C infection.