Differential lncRNA expression profiles reveal the potential roles of lncRNAs in antiviral immune response of Crassostrea gigas

Core genes of biomineralization and cis-regulatory long non-coding RNA regulate shell growth in bivalves

INTRODUCTION

Bivalve molluscs are abundant in marine and freshwater systems and contribute essential ecosystem services. They are characterized by an exuberant diversity of biomineralized shells and typically have two symmetric valves (a.k.a shells), but oysters (Ostreidae), some clams (Anomiidae and Chamidae) and scallops (Pectinida) have two asymmetrical valves. Predicting and modelling the likely consequences of ocean acidification on bivalve survival, biodiversity and aquaculture makes understanding shell biomineralization and its regulation a priority.

OBJECTIVES

This study aimed to a) exploit the atypical asymmetric shell growth of some bivalves and through comparative analysis of the genome and transcriptome pinpoint candidate biomineralization-related genes and regulatory long non-coding RNAs (LncRNAs) and b) demonstrate their roles in regulating shell biomineralization/growth.

METHODS

Meta-analysis of genomes, de novo generated mantle transcriptomes or transcriptomes and proteomes from public databases for six asymmetric to symmetric bivalve species was used to identify biomineralization-related genes. Bioinformatics filtering uncovered genes and regulatory modules characteristic of bivalves with asymmetric shells and identified candidate biomineralization-related genes and lncRNAs with a biased expression in asymmetric valves. A shell regrowth model in oyster and gene silencing experiments, were used to characterize candidate gene function.

RESULTS

Shell matrix genes with asymmetric expression in the mantle of the two valves were identified and unique cis-regulatory lncRNA modules characterized in Ostreidae. LncRNAs that regulate the expression of the tissue inhibitor of metalloproteinases gene family (TIMPDR) and of the shell matrix protein domain family (SMPDR) were identified. In vitro and in vivo silencing experiments revealed the candidate genes and lncRNA were associated with divergent shell growth rates and modified the microstructure of calcium carbonate (CaCO3) crystals.

CONCLUSION

LncRNAs are putative regulatory factors of the bivalve biomineralization toolbox. In the Ostreidae family of bivalves biomineralization-related genes are cis-regulated by lncRNA and modify the planar growth rate and spatial orientation of crystals in the shell.

Transcriptomic and functional analysis of the antiviral response of mussels after a poly I:C stimulation

The study of mussels (Mytilus galloprovincialis) has grown in importance in recent years due to their high economic value and resistance to pathogens. Because of the biological characteristics revealed by mussel genome sequencing, this species is a valuable research model. The high genomic variability and diversity, particularly in immune genes, may be responsible for their resistance to pathogens found in seawater and continuously filtered and internalized by them. These facts, combined with the lack of proven mussel susceptibility to viruses in comparison to other bivalves such as oysters, result in a lack of studies on mussel antiviral response. We used RNA-seq to examine the genomic response of mussel hemocytes after they were exposed to poly I:C, simulating immune cell contact with viral dsRNA. Apoptosis and the molecular axis IRFs/STING-IFI44/IRGC1 were identified as the two main pathways in charge of the response but we also found a modulation of lncRNAs. Finally, in order to obtain new information about the response of mussels to putative natural challenges, we used VHSV virus (Viral Hemorrhagic Septicemia Virus) to run some functional analysis and confirm poly I:C's activity as an immunomodulator in a VHSV waterborne stimulation. Both, poly I:C as well as an injury stimulus (filtered sea water injection) accelerated the viral clearance by hemocytes and altered the expression of several immune genes, including IL-17, IRF1 and viperin.

Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis

Noncoding RNAs (ncRNAs) have gained significant attention in recent years due to their crucial roles in various biological processes. However, our understanding of the expression and functions of ncRNAs in Cyclina sinensis, an economically important marine bivalve, remains limited. This study aimed to address this knowledge gap by systematically identifying ncRNAs in the mantles of C. sinensis with purple and white shells. Through our analysis, we identified a differential expression of 1244 mRNAs, 196 lncRNAs, 49 circRNAs, and 23 miRNAs between purple- and white-shell clams. Functional enrichment analysis revealed the involvement of these differentially expressed ncRNAs in biomineralization and pigmentation processes. To gain further insights into the regulatory mechanisms underlying shell color formation, we established competitive endogenous RNA (ceRNA) networks. These networks allowed us to identify targeted differentially expressed miRNAs (DEMis) and genes associated with shell color formation. Based on the ceRNA networks, we obtained an up-down-up lncRNA-miRNA-mRNA network consisting of 13 upregulated lncRNAs and a circRNA-miRNA-mRNA network comprising three upregulated circRNAs (novel_circ_0004787, novel_circ_0001165, novel_circ_0000245). Through these networks, we identified and selected an upregulated novel gene (evm.TU.Hic_asm_7.988) and a downregulated sponge miRNA (hru-miR-1985) as potential contributors to shell color regulation. In summary, the present investigation offers a comprehensive analysis of ncRNA catalogs expressed in the clam mantle of C. sinensis. The findings enhance our comprehension of the molecular mechanisms governing shell coloration and offer new perspectives for selective breeding of C. sinensis in the future.

Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone

Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.

Epigenetic variation mediated by lncRNAs accounts for adaptive genomic differentiation of the endemic blue mussel Mytiluschilensis

Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cochamó (41°S) and Yaldad (43°S), southern Chile, both impacted by climatic-related conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 % of the gill transcriptome and 1.96 % of the mantle transcriptome, representing an average of 2.76 % of the whole transcriptome. Using a high fold change value (≥|100|), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cochamó and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cochamó (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations.

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

BACKGROUND

Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species has recently been seriously affected by the frequent outbreaks of Polydora disease, causing great economic losses. Long non-coding RNAs (lncRNAs) exhibit exhibit crucial effects on diverse biological processes, but still remain poorly studied in scallops, limiting our understanding of the molecular regulatory mechanism of P. yessoensis in response to Polydora infestation.

RESULTS

In this study, a high-throughput transcriptome analysis was conducted in the mantles of healthy and Polydora-infected P. yessoensis by RNA sequencing. A total of 19,133 lncRNAs with 2,203 known and 16,930 novel were identified. The genomic characterizations of lncRNAs showed shorter sequence and open reading frame (ORF) length, fewer number of exons and lower expression levels in comparison with mRNAs. There were separately 2280 and 1636 differentially expressed mRNAs and lncRNAs (DEGs and DELs) detected in diseased individuals. The target genes of DELs were determined by both co-location and co-expression analyses. Functional enrichment analysis revealed that DEGs involved in melanization and biomineralization were significantly upregulated; further, obviously increased melanin granules were observed in epithelial cells of the edge mantle in diseased scallops by histological and TEM study, indicating the crucial role of melanizaiton and biomineralization in P. yessoensis to resist against Polydora infestation. Moreover, many key genes, such as Tyrs, Frizzled, Wnts, calmodulins, Pifs, perlucin, laccase, shell matrix protein, mucins and chitins, were targeted by DELs. Finally, a core lncRNA-mRNA interactive network involved in melanization and biomineralization was constructed and validated by qRT-PCR.

CONCLUSIONS

This work provides valuable resources for studies of lncRNAs in scallops, and adds a new insight into the molecular regulatory mechanisms of P. yessoensis defending against Polydora infestation, which will contribute to Polydora disease control and breeding of disease-resistant varieties in molluscs.

Mussel antiviral transcriptome response and elimination of viral haemorrhagic septicaemia virus (VHSV)

As filter-feeding bivalves, mussels have been traditionally studied as possible vectors of different bacterial or viral pathogens. The absence of a known viral pathogen in these bivalves makes it particularly interesting to study the interaction of the mussel innate immune system with a virus of interest. In the present work, mussels were challenged with viral haemorrhagic septicaemia virus (VHSV), which is a pathogen in several fish species. The viral load was eliminated after 24 h and mussels evidenced antiviral activity towards VHSV, demonstrating that the virus was recognized and eliminated by the immune system of the host and confirming that mussels are not VHSV vectors in the marine environment. The transcriptome activating the antiviral response was studied, revealing the involvement of cytoplasmic viral sensors with the subsequent activation of the JAK-STAT pathway and several downstream antiviral effectors. The inflammatory response was inhibited with the profound downregulation of MyD88, shifting the immune balance towards antiviral functions. High modulation of retrotransposon activity was observed, revealing a mechanism that facilitates the antiviral response and that had not been previously observed in these species. The expression of several inhibitors of apoptosis and apoptosis-promoting genes was modulated, although clear inhibition of apoptosis in bivalves after severe viral infection and subsequent disease was not observed in this study. Finally, the modulated expression of several long noncoding RNAs that were correlated with genes involved in the immune response was detected.

The potential role of eyestalk in the immunity of Litopenaeus vannamei to Vibrio parahaemolyticus infection II. From the perspective of long non-coding RNA

Long non-coding RNAs (lncRNAs) have been linked to immunological modulation. Unfortunately, little is known about the processes of immune control in shrimp. In crustaceans such as Litopenaeus vannamei, a prominent aquaculture species, the X-organ-sinus gland complex (XO-SG) in the eyestalk is an essential neuroendocrine regulatory organ. Eyestalk ablation is commonly employed in aquaculture to accelerate ovarian maturation in shrimp. It does, however, have a negative impact on the shrimps' immunocompetence and causes death. As a result, we used RNA-seq to profile the transcriptomes of L. vannamei hemocytes infected with Vibrio parahaemolyticus after the eyestalk ablation. Following strict transcript screening procedures, 2307 lncRNAs were identified from L. vannamei hemocytes in this study. Pearson correlation analysis was finally used to uncover 535 DElncRNAs and 1566 DEmRNA targets. According to the Venn diagram analysis, 326 non-eyestalk regulatory lncRNAs (NElncRNAs) with a target of 1014 non-eyestalk regulatory genes (NEmRNAs), 47 eyestalk negative regulatory lncRNAs (ENRlncRNAs) with a target of 95 eyestalk negative regulatory genes (ENRmRNAs), and 162 eyestalk positive regulatory lncRNAs (EPRlncRNAs) with a target of 457 eyestalk positive regulatory genes (EPRmRNAs) were screened. The bioinformatics analysis revealed that lncRNAs were associated with Axon regeneration, Rap1 signaling pathway, Thyroid hormone signaling pathway, TGF-beta signaling pathway, and PI3K-Akt signaling pathway, implying that lncRNAs may play a role in the regulation of the neuroendocrine-immune (NEI) system. Furthermore, several lncRNAs targeting HSP70, YWHAZ, FER2, HIF1α, and Notch were discovered and verified by qRT-PCR. These findings showed that regulation of lncRNAs in hemocytes which were controlled by the eyestalk might be one of the impact variables in controlling the differential expression of mRNAs associated with immune response in L. vannamei infected with V. parahaemolyticus.

Long-read RNA sequencing of Pacific abalone Haliotis discus hannai reveals innate immune system responses to environmental stress

Haliotis discus hannai is a commercially important mollusk species, and the abalone aquaculture sector has been jeopardized by deteriorating environmental circumstances such as bacterial infection and thermal stress during the hot summers. However, due to a paucity of genetic information, such as transcriptome resources, our understanding of their stress adaptation is restricted. In this research, using single-molecule long-read (SMRT) sequencing technology, a library composed of ten tissues (i.e., haemocytes, gills, muscle, hepatopancreas, digestive tract, mantle, mucous gland, ovary, testis and head) was constructed and sequenced. In all, 41,855 high-quality unique transcripts, among which 24,778 were successfully annotated. Additionally, 13,463 SSRs, 1,169 transcription factors, and 18,124 lncRNAs were identified in H. discus hannai transcriptome. Furthermore, multiple immune-related transcripts were identified according to KEGG annotation, and a portion of these transcripts were mapped into several classical immune-related pathways, including the PI3K-AKT signaling pathway and Toll-like receptor signaling pathway. Additionally, 24 typical sequences related to the immunity pathway were detected by RT-PCR; the results showed that most of the immune-related genes showed significantly high expression at 72 h after bacterial challenges and thermal stress, especially the expression level of genes in gills was significantly higher than that in haemocytes under V. parahaemolyticus stress at 24 h. At the same time. The analysis of alternative splicing identified several innate immunity-related functions genes, including CD109 and caspase 2. These results suggest that the complex immune system, particularly the powerful innate immunity system, was crucial for H. discus hannai response to numerous environmental challenges.

Full-length transcriptome sequencing of Heliocidaris crassispina using PacBio single-molecule real-time sequencing

The lack of high-throughput sequencing data makes the research progress of Heliocidaris crassispina slow. Therefore, we used PacBio single-molecule real-time sequencing to generate the first full-length transcriptome. Here, 31,181 isoforms were obtained, with an average length of 2383.20 and a N50 length of 2732 bp. Meanwhile, 764 alternative splicing (AS) events, 5098 long-noncoding RNAs (LncRNAs), 6978 simple sequence repeats (SSRs), and 950 hypothetical transcript factors (TFs) were identified. Moreover, five key innate immune pattern recognition receptors (PRRs), including toll-like receptor (TLR), NACHT domain and leucine-rich repeat (NLR), scavenger receptor cysteine-rich (SRCR), peptidoglycan recognition proteins (PGRP), and gram-negative binding proteins (GNBP), were searched in the transcriptome. In addition, 37 isoforms enriched in KEGG and GO immune systems were also detected. The study provid abundant data support for the current research on H. crassispina.

Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida

Aeromonas salmonicida (A. salmonicida) is a pathogenic bacterium that causes serious problems in the global Atlantic salmon aquaculture industry. In this study, we comprehensively analyzed the profiles of lncRNAs, miRNAs and mRNAs in gills of Atlantic salmon at high-dose A. salmonicida infection (3.06 × 10⁸ CFU/mL), low-dose A. salmonicida infection (3.06 × 10⁵ CFU/mL), and a PBS (100 μL) control. We identified 65 differentially expressed lncRNAs, 41 miRNAs, and 512 mRNAs between the control group and infection groups. Functional analysis showed that these genes were significantly enriched in the p53 signaling pathway, Wnt signaling pathway, mTOR signaling pathway, JAK-STAT signaling pathway, and Toll-like receptor signaling pathway. In addition, we predicted key genes in immune-related pathways and constructed a lncRNA-miRNA-mRNA network based on whole transcriptomic analysis. We further predicted three lncRNA-miRNA-mRNA axes as potential novel biomarkers in regulating the immune response of Atlantic salmon against A. salmonicida infection.

Integrated analysis of mRNA and long non-coding RNA expression profiles reveals the potential roles of lncRNA-mRNA network in carp macrophage immune regulation

Long non-coding RNAs (lncRNAs) have emerged as a hot topic in research as mounting evidence has indicated their transcriptional or post-transcriptional regulatory potential in multiple biological processes. Previous studies have revealed the involvement of lncRNAs in the immunoregulation of mammalian macrophages by changing mRNA expression; however, studies on the lncRNAs in fish macrophages and their potential roles in the immune system remain unknown. Primary macrophages were isolated from the head kidney (HK) of red common carp (Cyprinus carpio) and high-throughput lncRNA-mRNA sequencing was performed using the Illumina HiSeq platform. The results revealed that the most highly expressed mRNAs in primary HK macrophages were mainly involved in immune-related signal pathways. Furthermore, the most enriched immune-related GO term and KEGG pathway of the mRNAs were "immune system development" and "chemokine signaling pathway," respectively. A total of 20,333 lncRNAs, composed of 10,512 known and 9821 novel lncRNAs, were identified, and functional enrichment analysis of the lncRNA-mRNA network indicated that the expressed lncRNAs in primary HK macrophages could be associated with the regulation of multiple immune-related signaling pathways. In addition, the expressions of several selected lncRNAs and their related mRNAs were determined in carp macrophages following a 6-h exposure to lipopolysaccharide (LPS) and Poly(I: C), the results of which confirmed the co-expression regulation of lncRNAs and target mRNAs in the immune response of carp macrophages. These results suggest the correlative of the lncRNA-mRNA network in fish macrophage immune response, which may further affect the cross-talk of various signaling pathways by interaction with other network genes. Here, we provided fundamental data about the transcriptome profiles of primary HK macrophages from red common carp by analysis of the lncRNA-mRNA network, and ultimately suggest the potential roles of lncRNA-mRNA networks in immune regulation in teleost fish.

Differential Expression of Long Non-Coding RNA (lncRNA) in Mediterranean Mussel (Mytilus galloprovincialis) Hemocytes under Immune Stimuli

The Mediterranean mussel is one of the most economically relevant bivalve mollusk species in Europe and China. The absence of massive mortalities and their resistance to pathogens affecting other cultured bivalves has been under study in recent years. The transcriptome response of this species to different immune stimuli has been extensively studied, and even the complexity of its genome, which has recently been sequenced, has been suggested as one of the factors contributing to this resistance. However, studies concerning the non-coding RNA profiles remain practically unexplored-especially those corresponding to the lncRNAs. To the best of our knowledge, this is the second characterization and study of lncRNAs in this bivalve species. In this work, we identified the potential repertoire of lncRNAs expressed in mussel hemocytes, and using RNA-Seq we analyzed the lncRNA profile of mussel hemocytes stimulated in vitro with three different immune stimuli: LPS, poly I:C, and β-glucans. Compared to unstimulated hemocytes, LPS induced the highest modulation of lncRNAs, whereas poly I:C and β-glucans induced a similar discrete response. Based on the potential cis-regulatory activity of the lncRNAs, we identified the neighboring protein-coding genes of the regulated lncRNAs to estimate-at least partially-the processes in which they are implicated. After applying correlation analyses, it seems that-especially for LPS-the lncRNAs could participate in the regulation of gene expression, and substantially contribute to the immune response.

Integrative Transcriptomic Analysis Reveals the Immune Mechanism for a CyHV-3-Resistant Common Carp Strain

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp developed resistance to CyHV-3 infection. This study illustrates the immune mechanisms involved in both sensitivity and anti-virus ability for CyHV3 infection in fish. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at days 0 (the healthy control) and 7 after CyHV-3 infection (the survivors) and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. To dig out details on the immune aspect, the DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops a marked resistance to CyHV-3 infection through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune-suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3), as well as galectin 3 function by lncRNA, may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

Differentially expressed lncRNAs involved in immune responses of Haliotis diversicolor and H. discus hannai challenged with Vibrio parahaemolyticus

Although many studies have shown that lncRNA, a non-coding RNA with a length of more than 200 bases, is involved in various biological functions, including the immune process, stress process, and cell development process. However, the function of lncRNA in abalone, especially in immunity, has been rarely studied. H. discus hannai and H. diversicolor are two main aquaculture abalone, and their growth is easily affected by the main pathogen Vibrio parahaemolyticus. Through rigorous screening procedures for transcripts in this study, we found that lncRNAs were 34,240, 23,022 in Haliotis diversicolor and H. discus hannai injected with V. parahaemolyticus, respectively. We also identified the unique and common lncRNAs and mRNAs of two abalone species for the first time; the shared lncRNAs and mRNAs in Haliotis diversicolor and H. discus hannai were 2352 and 13,165, respectively. Then gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed target genes of common and unique lncRNAs has shown that common lncRNAs could be widely involved in the biological processes of stress and cell development in both abalone species. In contrast, unique lncRNAs are linked to the Toll-like receptor, NF-kappaB signaling pathway of H. diversicolor, and pattern recognition receptors and lectins immune-related pathways of H. discus hannai. The co-expression network shows that some immune-related genes, such as INFK1, INFK2, CASP2, CASP8, IRAK1, lectin C, were closely related to lncRNAs. Further, we identified the targeted relationship between some immune-related genes and lncRNAs by qRT-PCR, through which we showed that the expression trend between targeted genes, such as INFK1 and Lnc7057, lectin C and Lnc6943, Lnc5637, and PLCG1 and Lnc1692, were consistent. In general, our results showed that lncRNA expression was induced in the two species of abalone after being infected with V. parahaemolyticus, and lncRNA was involved in the immune response of abalone by targeting coding genes.

Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection

Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in large yellow croaker (Larimichthys crocea) are still rare, and they lack systematic analysis. In this study, 101 RNA-seq datasets varied in ages, sexes, and tissues were retrieved from the NCBI database to generate a comprehensive catalog of large yellow croaker transcriptome database. A set of 14,599 high-confidence lncRNAs from 13,673 loci were identified and characterized. Furthermore, RNA-seq datasets obtained from the infection of C. irritans were employed to investigate the differential expression pattern of lncRNAs and analyze potential biological functions. A total of 77 differentially expressed lncRNAs targeting to 567 protein-coding genes were identified by using expression analysis. Several immune genes, including TLR5, CD2AP, and MMP9, were highlighted. With GO enrichment and KEGG pathway analysis, the immune-related terms or pathways were enriched. This study created a comprehensive dataset of lncRNAs for large yellow croaker, which would be helpful for the researches of functional roles of lncRNAs in large yellow croaker.

The functional roles of the non-coding RNAs in molluscs

This review focus on the current knowledge of non-coding RNAs (ncRNAs) in molluscs. In this review, we provide an overview of long ncRNAs (lncRNA), microRNAs (miRNA) and piwi-interacting RNAs (piRNA), followed by evidence for the regulation of ncRNAs in variety of biological process in molluscs, including development, biomineralization and innate immune response. This review advances our understanding on the roles of ncRNAs in molluscs and suggest the future direction to fully understand the epigenetic regulatory network of molluscs.

Identification of a long non-coding RNA (LncMSEN2) from pearl oyster and its potential roles in exoskeleton formation and LPS stimulation

Long non-coding RNAs (lncRNAs) play regulatory roles in various biological processes, including exoskeleton formation and immune response. The exoskeleton-based mantle-shell defense system is an important defense mechanism in shellfish. In this study, we found a novel lncRNA, herein formally named, LncMSEN2, from the pearl oyster Pinctada fucuta martensii, and its sequence was validated via polymerase chain reaction (PCR). LncMSEN2 was highly expressed in mantle tissues, especially in the central region (P < 0.05), and was also expressed in the pearl sac as detected by quantitative real-time PCR. In situ hybridization experiments revealed that LncMSEN2 had a strong positive signal in the inner and outer epidermal cells of the mantle pallial and central regions. RNA interference experiments showed that interference of LncMSEN2 expression with dsRNA in mantle tissues led to an abnormal crystal structure of the nacre. In addition, LncMSEN2 expression significantly increased 6 h after lipopolysaccharide stimulation in mantle tissues (P < 0.05). These results indicated that LncMSEN2 may be a novel regulator of the mantle-shell defense system of pearl oyster.

Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel (Genypterus chilensis) via RNA-seq

The red cusk-eel (Genypterus chilensis) is a native species with strong potential to support Chilean aquaculture diversification. Under commercial conditions, fish are exposed to several stressors. To date, little is known about the mechanism involved in the stress response of red cusk-eel, and there is no information related to the regulation mediated by long noncoding RNAs (lncRNAs). The objective of this work was to identify for the first time the lncRNAs in the transcriptome of G. chilensis and to evaluate the differential expression levels of lncRNAs in the liver, head kidney, and skeletal muscle in response to handling stress. We used previously published transcriptome data to identify the lncRNAs by applying a series of filters based on annotation information in several databases to discard coding sequences. We identified a total of 14,614 putative lncRNAs in the transcriptome of red cusk-eel, providing a useful lncRNA reference resource to be used in future studies. We evaluated their differential expression in response to handling stress in the liver, head kidney, and skeletal muscle, identifying 112, 323, and 108 differentially expressed lncRNAs, respectively. The results suggest that handling stress in red cusk-eel generate an altered metabolic status in liver, altered immune response in head kidney, and skeletal muscle atrophy through an important coding and noncoding gene network. This is the first study that identifies lncRNAs in Genypterus genus and that evaluates the relation between handling stress and lncRNAs in teleost fish, thereby providing valuable information regarding noncoding responses to stress in Genypterus species.

The global effects of PmRunt co-located and co-expressed with a lincRNA lncRunt in pearl oyster Pinctada fucata martensii

Runt related transcription factors as trans-acting elements play critical roles in the developmental control of cell fate, hematopoiesis, bone formation and cancers. In previous study, the homologue of runt related transcription factor PmRunt has been identified from pearl oyster Pinctada fucata martensii and considered to play an important role in nacre formation. In this study, we used the same samples to perform RNA-seq to detect the global effects after the decrease of PmRunt expression. The transcription levels of several nacre shell matrix protein (NSMP) genes were significantly changed and the potential compensatory effect could happen internal gene families. Downregulation of PmRunt could also influence the biosynthesis of NSMPs through affecting amino acid metabolism, translation, protein processing and export. The inhibition of PmRunt also possibly affected the expression of caspases, IAPs and C1qs that related to apoptosis and immune. In addition, PmRunt highly expressed at 12 h and 12 d after transplantation in hemolymph, which was corresponded to transplantation immunity immune response and the morphology of pearl sac, suggested the cross-talk of biomineralization-immune regulation in hemocytes. Furthermore, a lincRNA (LncRunt) that co-located with PmRunt was identified and showed a significantly relative expression with PmRunt, which suggested the potential regulation. Therefore, these findings provided new idea to find the regulation targets of runt-related transcription factors and offers evidence of lncRNAs in potential biomineralization-immune regulation.

A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks

Background

Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila.

Results

We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets.

Conclusions

We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.

Dual RNA-Seq Unveils Pseudomonas plecoglossicida htpG Gene Functions During Host-Pathogen Interactions With Epinephelus coioides

Pseudomonas plecoglossicida is a temperature-dependent opportunistic pathogen which is associated with a variety of diseases in fish. During the development of "white nodules" disease, the expression of htpG in P. plecoglossicida was found to be significantly up-regulated at its virulent temperature of 18°C. The infection of htpG-RNAi strain resulted in the onset time delay, reduction in mortality and infection symptoms in spleen of Epinephelus coioides, and affected the bacterial tissue colonization. In order to reveal the effect of htpG silencing of P. plecoglossicida on the virulence regulation in P. plecoglossicida and immune response in E. coioides, dual RNA-seq was performed and a pathogen-host integration network was constructed. Our results showed that infection induced the expression of host genes related to immune response, but attenuated the expression of bacterial virulence genes. Novel integration was found between host immune genes and bacterial virulence genes, while IL6, IL1R2, IL1B, and TLR5 played key roles in the network. Further analysis with GeneMANIA indicated that flgD and rplF might play key roles during the htpG-dependent virulence regulation, which was in accordance with the reduced biofilm production, motility and virulence in htpG-RNAi strain. Meanwhile, IL6 and IL1B were found to play key roles during the defense against P. plecoglossicida, while CELA2, TRY, CPA1, CPA2, and CPB1 were important targets for P. plecoglossicida attacking to the host.