RNA-Seq Analysis of the Antioxidant Status and Immune Response of Portunus trituberculatus Following Aerial Exposure

Metabolic adaptation of the clam Ruditapes philippinarum during air exposure and the positive effects of sodium nitroprusside pretreatment

The Manila clam (Ruditapes philippinarum), as one of the shellfish living in the intertidal zone, is known for its strong ability to withstand air exposure. Sodium nitroprusside (SNP), a donor of nitric oxide (NO), has been shown to be useful for antioxidant and immune regulation in aquatic animals. In this study, an untargeted metabolomics (LC-MS/MS) technique was employed for the first time in Manila clam to analyze the metabolic and histological impacts after air exposure and the positive effects of SNP pretreatment. During air exposure, a significant increase in taurine, L-glutamate, and several polyunsaturated fatty acids in clams was detected, which indicates that clams may experience inflammatory reactions, oxidative stress, and an increase in blood ammonia content. When clams were exposed to SNP for 6 h, arginine, spermine, L-glutamic acid, and glutathione content were all upregulated, indicating that the SNP exposure induced NO production and improved antioxidant capacity in clams. When the clams were exposed to air after SNP pretreatment, there were no significant differences in the levels of taurine, L-glutamate, or aliphatic acids between the experimental and control groups. Gill tissue was more severely damaged in clams directly exposed to air than in those that experienced air exposure after SNP pretreatment, especially in clams exposed to air for a long time (72 h). Both metabolomics and tissue section structure indicated that SNP pretreatment decreased the stress responses caused by air exposure in R. philippinarum. These findings provided fresh insights and a theoretical foundation for understanding the tolerance to air exposure and physiological functions of SNP (or NO) in R. philippinarum.

Synergistic modulation of neuroendocrine-inflammation pathway by microRNAs facilitates intertidal adaptation of molluscs

Neuroendocrine-immune system is an evolution-conserved regulatory network in maintaining the homeostasis of animals. While knowledge on the roles of neuroendocrine-immune system in the disease and stress responses of organisms is growing, the ecological roles of neuroendocrine-immune system, especially how it shapes the unique lifestyle of organisms remain insufficiently investigated. As an endemic and dominant mollusc in intertidal region, oysters have evolved with a primitive neuroendocrine-immune system and with a sessile lifestyle. Recently, a novel neuroendocrine-immune pathway, Ca2+/calmodulin (CaM)-nitrite oxide synthase (NOS)/nitrite oxide (NO)-tumor necrosis factor (TNF) pathway, is identified in oysters and found altered dynamically during aerial exposure, one common but challenging stresses for intertidal organisms and a decisive factor shaping their habitat. Since the pathway proves fatal in prolonged aerial exposure, we hypothesized that the activation/deactivation of pathway could be strictly modulated in adaptation to the sessile lifestyle of oysters. Here, a synergistic modulation on the Ca2+/CaM-NOS/NO-TNF pathway by four members of miR-92 family and two oyster-specific miRNAs was identified, which further hallmarks the resilience and survival strategy of oysters to aerial exposure. Briefly, these six miRNAs were down-regulating CgCaM24243 post-transcriptionally and deactivating the pathway during the early-stage of stress. However, a robust recession of these miRNAs occurred at the late-stage of stress, resulting in the reactivation of pathway and overwhelming accumulation of cytokines. These results demonstrated a complicated interaction between miRNAs and ancient neuroendocrine-immune system, which facilitates the environmental adaptation of intertidal oysters and provides novel insight on the function and evolution of neuroendocrine-immune system in ecological context.

Antioxidation, immunity and hepatopancreatic histology of red swamp crayfish (Procambarus clarkii) subjected to low-temperature aerial exposure stress and re-immersion

Desiccation is a stressful situation that decapods often experience during live transportation. This study investigated the effects of low-temperature aerial exposures (LTAEs) (dry exposure (DL) and moist exposure (ML) at 6 °C) and re-immersion on the antioxidative and immune responses and hepatopancreatic histopathology in P. clarkii. Compared to the control group (normally feeding at 24.0 °C water temperature), the crayfish under LTAEs showed overall severe hepatopancreatic oxidative damage, with significantly increased malondialdehyde (MDA) contents and significantly reduced total antioxidant capacity (T-AOC), and oxidant damage was not fully recovered even after 12 h of re-immersion; the expression of hsp70 was significantly increased within 24-48 h of stress and re-immersion. The activity of hemolymphatic acid phosphatase (ACP) was significantly increased during 24-48 h of the stress and at 12 h of re-immersion; the activity of aspartic aminotransferase (AST) and alanine aminotransferase (ALT) was significantly increased throughout the experiment; and the gene expression of proPO or TLR was significantly increased during 12-48 h of the stress. Severe histopathological changes (lumen dilatation, vacuolation of epithelial cells and reduced cell numbers) were observed in hepatopancreas at 48 h of stress and 12 h of re-immersion. These results indicated that 48 h of low-temperature aerial exposure stress stimulated the non-specific immunity but adversely affected the antioxidation and hepatopancreatic histomorphology of P. clarkii, whereas 12 h of re-immersion was not sufficient to restore crayfish from stress to a normal state.

Effects of high water temperature on physiology, survival, and resistance to high temperature air-exposure in the Manila clam Ruditapes philippinarum

Ruditapes philippinarum is a typical burrowing shellfish, living in the intertidal zone. In natural conditions, the mortality of R. philippinarum is most affected by high water temperatures, high temperature air-exposure, and other environmental stresses. In this study, the mortality rates of the two populations of R. philippinarum under high water temperature stress were recorded, and catalase (CAT), superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) antioxidant enzyme activities in the hepatopancreas were analyzed. The results showed that the survival times of cultured clams were longer than those of wild clams after acute high temperature stress. CAT, SOD, and T-AOC activities increased after acute high water temperature and high temperature air-exposure stress. These antioxidant enzyme activities gradually decreased to their initial levels after 2 days of recovery from these high temperature stresses. Based on these experimental results, we found that the cultured clam population had better heat and high temperature air-exposure resistances than the wild clams. CAT, SOD, and T-AOC enzymes play an important role in the antioxidant processes of R. philippinarum in response to high water temperature and high temperature air-exposure. This study provided a theoretical basis for the development of healthy aquacultural practices for these shellfish.

Full-Length Transcriptome Analysis Provides New Insights Into the Diversity of Immune-Related Genes in Portunus trituberculatus

Generally, invertebrates were thought to solely rely on their non-specific innate immune system to fight against invading microorganisms. However, increasing studies have implied that the innate immune response of invertebrates displayed diversity and specificity owing to the hyper-variable immune molecules in organisms. In order to get an insight into the diversity of immune-related genes in Portunus trituberculatus, a full-length transcriptome analysis of several immune-related tissues (hemocytes, hepatopancreas and gills) in P. trituberculatus was performed and the diversity of several immune-related genes was analyzed. The full-length transcriptome analysis of P. trituberculatus was conducted using a combination of SMRT long-read sequencing and Illumina short-read sequencing. A total of 17,433 nonredundant full-length transcripts with average length of 2,271 bp and N50 length of 2,841 bp were obtained, among which 13,978 (80.18%) transcripts were annotated. Moreover, numerous transcript variants of various immune-related genes were identified, including pattern recognition receptors, antimicrobial peptides, heat shock proteins (HSPs), antioxidant enzymes and vital molecules in prophenoloxidase (proPO)-activating system. Based on the full-length transcriptome analysis, open reading frames (ORFs) of four C-type lectins (CTLs) were cloned, and tissue distributions showed that the four CTLs were ubiquitously expressed in all the tested tissues, and mainly expressed in hepatopancreas and gills. The transcription of the four CTLs significantly increased in several immune-related tissues (hemocytes, hepatopancreas and gills) of P. trituberculatus challenged with Vibrio alginolyticus and displayed different profiles. Moreover, the four CTLs displayed distinct bacterial binding and antibacterial activities. The recombinant protein PtCTL-1 (rPtCTL-1) and rPtCTL-3 displayed bacterial binding and antibacterial activities against all tested bacteria. rPtCTL-2 only showed bacterial binding and antibacterial activities against V. alginolyticus. No obvious bacterial binding or antibacterial activities for PtCTL-4 was observed against the tested bacteria. This study enriches the transcriptomic information on P. trituberculatus and provides new insights into the innate immune system of crustaceans. Additionally, our study provided candidates of antibiotic agents for the prevention and treatment of bacteriosis.

Transcriptomic responses to air exposure stress in coelomocytes of the sea cucumber, Apostichopus japonicus

During rearing in hatcheries and transportation to restocking sites, sea cucumbers are often exposed to air for several hours, which may depress their non-specific immunity and lead to mass mortality. We performed transcriptome analysis of Apostichopus japonicus coelomocytes after air exposure to identify stress-related genes and pathways. After exposure to air for 1 h, individuals were re-submerged in aerated seawater and coelomocytes were collected at 0, 1, 4, and 16 h (B, H1, H4, and H16, respectively). We identified 6148 differentially expressed genes, of which 3216 were upregulated and 2932 were downregulated. Many genes involved in the immune response, antioxidant defense, and apoptosis were highly induced in response to air exposure. Enrichment analysis of Gene Ontology terms showed that the most abundant terms in the biological process category were oxidation-reduction process, protein folding and phosphorylation, and receptor-mediated endocytosis for the comparison of H1 vs. B, H4 vs. H1, and H16 vs. H4, respectively. Kyoto Eecyclopedia of Genes and Genomes enrichment analysis showed that six pathways related to the metabolism of proteins, fats, and carbohydrates were shared among the three comparisons. These results indicated that sea cucumbers regulate the expression of genes related to the antioxidant system and energy metabolism to resist the negative effects of air exposure stress. These findings may be applied to optimize juvenile sea cucumber production, and facilitate molecular marker-assisted selective breeding of an anoxia-resistant strain.

Immune and physiological responses of mud crab (Scylla paramamosain) under air exposure

The immune and physiological responses of mud crab (Scylla paramamosain) under air exposure were studied. The results showed that air exposure increased plasma activities of AST, ALT, ALP. There was a significant increase in glucose (GLU) and malondialdehyde (MDA) levels after air exposure. The transcript levels of SOD, CAT, HSP90, HSP70, p53, and hypoxia-inducible factor-1 (HIF-1) were induced by air exposure. Furthermore, caspase-3 transcript significantly increased at 48 and 72 h, while it significantly decreased at 96 h and 120 h under air exposure. These results suggested that oxidative stress occurred in the prolonged period of air exposure. HIF-1 and p53 signaling pathways played an important role under air exposure.

Modulated Expression and Activities of Ruditapes philippinarum Enzymes After Oxidative Stress Induced by Aerial Exposure and Reimmersion

Ruditapes philippinarum, is an economically and scientifically important bivalve mollusk. Its tolerance of aerial exposure has long been considered an important trait for its survival under acute environmental stress. In this study, the effects of air exposure at high and low temperatures (28 and 4°C) on the survival, antioxidant and metabolic enzyme activities, and the expression of antioxidant and immune-related genes in R. philippinarum were investigated. The activities of antioxidant and metabolic enzymes [superoxide dismutase (SOD), α-amylase, and proline hydroxylase (PHD)] were significantly affected by aerial exposure and reimmersion (reoxygenation) at both low (4°C) and high (28°C) temperatures. Moreover, the mRNA expression of α-amylase, SOD, and C-type lectin was also examined, which reveals these genes were significantly affected by aerial exposure challenge. In addition, the effects of aerial exposure and reimmersion on survival rate were calculated to evaluate the recovery capacity of Manila clam after aerial exposure at high and low temperatures. All individuals survived under low temperature aerial exposure for 24 h and reimmersion for 120 h. However, individuals died after reimmersion for 12 h following high temperature aerial exposure, and mortality peak occurred at 48 h. These data indicate that long-term aerial exposure during the transportation of clams should be in a low temperature environment. This study demonstrates that enzyme expression and activities linked to the stress response increase during the aerial exposure of R. philippinarum and provide useful information for future work on the molecular basis of tolerance of aerial exposure stress.

Genome-Wide Characterization of Alternative Splicing Events and Their Responses to Cold Stress in Tilapia

Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.

The Single-molecule long-read sequencing of Scylla paramamosain

Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S. paramamosain, which will greatly facilitate S. paramamosain research.

Physiological and immunological responses of sea cucumber Apostichopus japonicus during desiccation and subsequent resubmersion

Desiccation is one of the extremely stressful situations experienced by aquatic animals, and sea cucumber usually suffers from desiccation stress during transportation without water. The present study was conducted to evaluate the effect of desiccation and subsequent resubmersion on physiological stress, oxidative damage, antioxidant status and non-specific immune response of Apostichopus japonicus, providing valuable information on the health management of sea cucumber culturing. Control and desiccation groups were set up, and each group has three replicates. After 1, 3 and 6 h of desiccation, individuals were resubmersed in aerated seawater for a 24 h recovery in three batches, which were represented as D1, D3 and D6, respectively. The results showed that glucose level in coelomic fluid of sea cucumber significantly decreased after desiccation, whereas lactate, cortisol and osmolality showed remarkable ascending trends. Thereafter, all stress parameters gently recovered towards normal levels as control group during 24 h resubmersion. The prolonged desiccation at D6 treatment induced the significant increases of malondialdehyde (MDA) and reactive oxygen species (ROS) contents, as well as relatively lower superoxide dismutase (SOD) and catalase (CAT) activities. During the period of desiccation and subsequent resubmersion, sea cucumber adjusted antioxidant defense to reduce the concentrations of MDA and ROS as a strategy for protecting against oxidative damage. Desiccation also had significant effects on non-specific immune parameters (total coelomocytes counts, TCC; complement C3; total nitric oxide synthase, T-NOS; lysozyme, LSZ; alkaline phosphatase, AKP) of A. japonicus, which could be recovered to some extent during resubmersion. In conclusion, less than 6 h of desiccation did not induce irreparable damage to sea cucumber, and was recommended for handling and shipping live sea cucumbers.

Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq

Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.

Identification of immune-related genes in gills of Chinese mitten crabs (Eriocheir sinensis) during adaptation to air exposure stress

The Chinese mitten crab, Eriocheir sinensis, is the most important crab in China. Air exposure is regarded as one of the crucial restriction factors in the crab cultivation and transportation process. Numerous studies have shown that air exposure stress can cause many negative effects on aquatic farming animals. However, the molecular mechanisms of drying on Chinese mitten crabs are still poorly studied. In this study, gill reference transcriptome was assembled and differentially expressed gene (DGE) analysis was conducted between air exposure 16 h and normal dissolved oxygen of Chinese mitten crab. A total of 76075 transcripts were generated and 50800 unigenes with a mean length of 1090 bp and N50 length of 1584 bp were observed. Transcriptomic comparison revealed 352 DEGs between air exposure 16 h group and control group, including 122 up-regulated genes and 230 down-regulated genes. Gene ontology (GO) analysis revealed that these DEGs involved in 16 biological process subcategories, 8 cellular component subcategories and 6 molecular function subcategories. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis annotated 352 DEGs to 85 pathways, and some pathways were regarded as related with immune system and diseases, such as phagosome, systemic lupus erythematosus, and alcoholism. Eight genes involved in multiple KEGG signaling pathways were validated by qRT-PCR. This study demonstrates the first gill transcriptomic analysis challenged with air exposure stress in Chinese mitten crab and provides valuable gene resources for understanding the crab gill immunity, which can provides insight into the immune response of crab against air exposure stress.

Gonadal Transcriptome Analysis of Pacific Abalone Haliotis discus discus: Identification of Genes Involved in Germ Cell Development

Little is known about the molecular mechanisms governing gonadal developmental processes in abalones. Here, we conducted transcriptome analysis of Pacific abalone Haliotis discus discus for gene discovery in the brain, ovary, testis, and unfertilized eggs. Among the annotated unigenes, 48.6% of unigenes were identified by Venn diagram analysis as having universal or tissue-specific expression. Twenty-three genes with gonad-biased gene ontology (GO) terms were first obtained. Secondly, 36 genes were found by screening known gene names related to germ cell development. Finally, 17 genes were obtained by querying the annotated unigene database for zygotically expressed gonadal genes (ovary and testis) and maternally expressed gonadal genes (ovary, testis, and unfertilized eggs) using keywords related to reproduction. To further verify tissue distribution pattern and subcellular localization of these genes, RT-PCR and in situ hybridization were performed using a unigene encoding a germ cell marker, vasa, as control. The results showed that vasa was expressed mainly in the early developmental stages of germ cells in both sexes. One of the candidate genes, vitelline envelope zona pellucida domain protein 12 (ZP12), was expressed in the primordial germ cells of immature gonad and early developmental stages of germ cells of the adult female. The results obtained from the present study suggest that vasa and ZP12 are involved in germ cell development of Pacific abalone and that ZP12 is an especially useful germ cell-specific marker in immature adults. The current gonadal transcriptome profile is an extensive resource for future reproductive molecular biology studies of this species.

Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids

Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.