Transcriptome Analysis of the Hepatopancreas in the Pacific White Shrimp (Litopenaeus vannamei) under Acute Ammonia Stress

PvGeneExpDB: An integrative gene expression database for in-depth understanding on the Pacific white shrimp (Litopenaeus vannamei)

The Pacific white shrimp (Litopenaeus vannamei) is a high-valued economic farming species. With the development of high-throughput sequencing technology, cumulative large-scale transcriptomic studies have been revealing molecular landscape of various biological conditions including genetic selection, breeding, evolution, disease landscape, etc. However, no single experiment or databases allow thorough investigations of transcriptomic dynamics for these progressions. Meanwhile, the available datasets are often scattered and lack management. Here, we have established PvGeneExpDB, the first gene expression database for L. vannamei (www.bio-marine-scau.com/pv_ex/), which encompasses gene expression profiles, differential expression, and co-expression analyses under various biological conditions. Based on the analyses of 7 datasets, which include 53 samples with accurate and detailed records, PvGeneExpDB identifies 20,599 novel transcripts, shows expression profiles of a total of 20,817 genes, and implements Gene Ontology (GO) reconstruction of 76.7 % of these genes. Besides, 26 co-expressed groups were first identified by large-scale, cross-sample Weighted Gene Co-expression Network Analysis (WGCNA). By integrating the gene expression data in the database, our goal is to deepen the biological understanding of L. vannamei.

Synergistic effects of combined probiotics Bacillus pumilis D5 and Leuconostoc mesenteroide B4 on immune enhancement and disease resistance in Litopenaeus vannamei

This study investigated the effects of two distinct probiotics, Leuconostoc mesenteroides B4 (B4) and Bacillus pumilus D5 (D5), along with their combination, on the diet of white shrimp (Litopenaeus vannamei) during an eight-week feeding trial. The diets tested included B4 + dextran at 107 CFU/g feed (the B4 group), D5 alone at 107 CFU/g feed (the D5 group), and a combination of B4 + dextran and D5 at 5 × 106 CFU/g feed each (the B4+dextran + D5 group). Relative to the control group, those administered probiotics exhibited moderate enhancements in growth. By the eighth week, the weight gain for the B4, D5, and B4+D5 groups was 696.50 ± 78.15%, 718.53 ± 130.73%, and 693.05 ± 93.79%, respectively, outperforming the control group's 691.66 ± 31.10% gain. The feed conversion ratio was most efficient in the B4 group (2.16 ± 0.06), closely followed by B4+D5 (2.21 ± 0.03) and D5 (2.22 ± 0.06), with the control group having the highest ratio (2.27 ± 0.03). While phenoloxidase activity was somewhat elevated in the B4 and D5 groups, no significant differences were noted in respiratory burst activity or total hemocyte count across all groups. Challenge tests at weeks 4 and 8 showed that the B4 + D5 combination offered superior protection against AHPND-causing Vibrio parahaemolyticus. The 4-week cumulative survival rate was highest in shrimp treated with B4 + dextran + D5 (56.25%), followed by B4 + dextran (31.25%), control (18.75%), and lowest in D5 (12.5%). By week 8, the B4 + dextran + D5 (43.75%) and B4 + dextran (37.5%) groups significantly outperformed the control group (6.25%, p < 0.05), with no significant difference observed between the D5 group (37.5%) and the control group at day 56. Analysis of the shrimp's foregut microbiota revealed an increase in unique OTUs in the B4 and B4 + D5 groups. Compared to the control, Proteobacteria abundance was reduced in all probiotic groups. Potential pathogens like Vibrio, Bacteroides, Neisseria, Botrytis, Clostridioides, and Deltaentomopoxvirus were detected in the control but were reduced or absent in probiotic groups. Beneficial microbes such as Methanobrevibacter and Dictyostelium in the B4+D5 group, and Sugiyamaella in the B4 group, showed significant increases. Probiotics also led to higher transcript levels of nitric oxide synthase in the hemocytes, and lysozyme and transglutaminase in the midgut, along with lysozyme and α2-macroglobulin in the foregut. Notably, the combined B4 + D5 probiotics synergistically enhanced the expression of superoxide dismutase and prophenoloxidase in the foregut, indicating an improved immune response. In summary, this study demonstrates that the probiotics evaluated, especially when used in combination, significantly boost the expression of specific immune-related genes, enhance the bacterial diversity and richness of the intestine, and thus prevent the colonization and proliferation of Vibrio spp. in L. vannamei.

Penaeid shrimp counteract high ammonia stress by generating and using functional peptides from hemocyanin, such as HMCs27

Agricultural and anthropogenic activities release high ammonia levels into aquatic ecosystems, severely affecting aquatic organisms. Penaeid shrimp can survive high ammonia stress conditions, but the underlying molecular mechanisms are unknown. Here, total hemocyanin and oxyhemocyanin levels decreased in Penaeus vannamei plasma under high ammonia stress. When shrimp were subjected to high ammonia stress for 12 h, 24 hemocyanin (HMC) derived peptides were identified in shrimp plasma, among which one peptide, designated as HMCs27, was chosen for further analysis. Shrimp survival was significantly enhanced after treatment with the recombinant protein of HMCs27 (rHMCs27), followed by high ammonia stress. Transcriptome analysis of shrimp hepatopancreas after treatment with or without rHMCs27 followed by high ammonia stress revealed 973 significantly dysregulated genes, notable among which were genes involved in oxidation and metabolism, such as cytochrome C, catalase (CAT), isocitrate dehydrogenase, superoxide dismutase (SOD), trypsin, chymotrypsin, glutathione peroxidase, glutathione s-transferase (GST), and alanine aminotransferase (ALT). In addition, levels of key biochemical indicators, such as SOD, CAT, and total antioxidant capacity (T-AOC), were significantly enhanced, whereas hepatopancreas malondialdehyde levels and plasma pH, NH3, GST, and ALT levels were significantly decreased after rHMCs27 treatment followed by high ammonia stress. Moreover, high ammonia stress induced hepatopancreas tissue injury and apoptosis, but rHMCs27 treatment ameliorated these effects. Collectively, the current study revealed that in response to high ammonia stress, shrimp generate functional peptides, such as peptide HMCs27 from hemocyanin, which helps to attenuate the ammonia toxicity by enhancing the antioxidant system and the tricarboxylic acid cycle to decrease plasma NH3 levels and pH.

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

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

A review of the toxic effects of ammonia on invertebrates in aquatic environments

Aquatic invertebrates are the organisms most susceptible to ammonia toxicity. However, the toxic effects of ammonia on invertebrates are still poorly understood. This study reviews the research progress in ammonia toxicology for the period from 1986 to 2023, focusing on the effects on invertebrates. Through examining the toxic effects of ammonia at different levels of organization (community, individual, tissue and physiology, and molecular) as well as the results from omics studies, we determined that the most significant effects were on the reproductive capacity of invertebrates and the growth of offspring, although different populations show variation in their tolerance to ammonia, and tissues have varied potential to respond to ammonia stress. A multicomponent analysis is an in-depth technique employed in toxicological studies, as it can be used to explore the enrichment pathways and functional genes expressed under ammonia stress. This study comprehensively discusses ammonia toxicity from multiple aspects in order to provide new insights into the toxic effects of ammonia on aquatic invertebrates.

Dynamic N6-methyladenosine RNA methylation landscapes reveal epi-transcriptomic modulation induced by ammonia nitrogen exposure in the Pacific whiteleg shrimp Litopenaeus vannamei

Despite the versatility of RNA m⁶A methylation in regulating various biological processes, its involvement in the physiological response to ammonia nitrogen toxicity in decapod crustaceans like shrimp remains enigmatic. Here, we provided the first characterization of dynamic RNA m⁶A methylation landscapes induced by toxic ammonia exposure in the Pacific whiteleg shrimp Litopenaeus vannamei. The global m⁶A methylation level showed significant decrease following ammonia exposure, and most of the m⁶A methyltransferases and m⁶A binding proteins were significantly repressed. Distinct from many well-studied model organisms, m⁶A methylated peaks in the transcriptome of L. vannamei were enriched not only near the termination codon and in the 3' untranslated region (UTR), but also around the start codon and in the 5' UTR. Upon ammonia exposure, 11,430 m⁶A peaks corresponding to 6113 genes were hypo-methylated, and 5660 m⁶A peaks from 3912 genes were hyper-methylated. The differentially methylated genes showing significant changes in expression were over-represented by genes associated with metabolism, cellular immune defense and apoptotic signaling pathways. Notably, the m⁶A-modified ammonia-responsive genes encompassed a subset of genes related to glutamine synthesis, purine conversion and urea production, implying that m⁶A methylation may modulate shrimp ammonia stress responses partly through these ammonia metabolic processes.

First transcriptome profiling in gill and hepatopancrease tissues of Metapenaeus ensis in response to acute ammonia-N stress

The greasyback shrimp, Metapenaeus ensis, suffers from ammonia-N stress during intensive factory aquaculture. Optimizing ammonia-N stress tolerance has become an important issue in M. ensis breeding. The metabolic and adaptive mechanisms of ammonia-N toxicity in M. ensis have not been comprehensively understood yet. In this study, a large number of potential simple sequence repeats (SSRs) in the transcriptome of M. ensis were identified. Differentially expressed genes (DEGs) in the gill and hepatopancreas at 24 h post-challenges under high concentrations of ammonia-N treatment were detected. We obtained 20,108,851-27,681,918 clean reads from the control and high groups, assembled and clustered a total of 103,174 unigenes with an average of 876 bp and an N50 of 1189 bp. Comparative transcriptome analyses identified 2000 different expressed genes in the gill and 2010 different expressed genes in the hepatopancreas, a large number of which were related to immune function, oxidative stress, metabolic regulation, and apoptosis. The results suggest that M. ensis may counteract ammonia-N toxicity at the transcriptome level by increasing the expression of genes related to immune stress and detoxification metabolism, and that selected genes may serve as molecular indicators of ammonia-N. By exploring the genetic basis of M. ensis' ammonia-N stress adaptation, we constructed the genetic networks for ammonia-N adaptation. These findings will accelerate the understanding of M. ensis' ammonia-N adaptation, contribute to the research of future breeding, and promote the level of factory aquaculture of M. ensis.

Transcriptional and metabolomic investigation of the stress response in snow crab during simulated transport condition (Chionoecetes opilio)

The molecular mechanisms underlying the stress response are poorly described in crustaceans. This includes the snow crab (Chionoecetes opilio), a commercially important stenotherm species distributed throughout the northern hemisphere. A better understanding of the stress response in C. opilio is desperately needed for commercial and conservation purposes. The purpose of this study was to investigate the transcriptional and metabolomic response of C. opilio exposed to stressors. Crabs were randomly assigned to 24 or 72 h treatment groups where they were exposed to conditions simulating live transport (handling and air exposure). A control group was kept in cold (2 °C) and well‑oxygenated saltwater. The hepatopancreas of the crabs was sampled to perform RNA-sequencing and high-performance chemical isotope labeling metabolomics. Differential gene expression analyses showed that classic crustaceans' stress markers, such as crustacean hyperglycemic hormones and heat shock proteins, were overexpressed in response to stressors. Tyrosine decarboxylase was also up-regulated in stressed crabs, suggesting an implication of the catecholamines tyramine and octopamine in the stress response. Deregulated metabolites revealed that low oxygen was an important trigger in the stress response as intermediate metabolites of the tricarboxylic acid cycle (TCA) accumulated. Lactate, which accumulated unevenly between crabs could potentially be used to predict mortality. This study provides new information on how stressors affect crustaceans and provides a basis for the development of stress markers in C. opilio.

Integrated physiological and transcriptome analysis reveals potential toxicity mechanism of haloxyfop-P-methyl to Chiromantes dehaani

Haloxyfop-P-methyl is widely used in controlling gramineous weeds, including the invasive plant Spartina alterniflora. However, the mechanism of its toxicity to crustaceans is unclear. In this study, we adopted transcriptome analysis combined with physiologic changes to investigate the response of estuarine crab (Chiromantes dehaani) to haloxyfop-P-methyl. The results showed that the median lethal concentration (LC₅₀) of C. dehaani to haloxyfop-P-methyl at 96 h was 12.886 mg/L. Antioxidant system analysis indicated that MDA, CAT, GR, T-GSH, and GSSG might be sensitive biomarkers that characterize the oxidative defense response of the crab. In total, 782 differentially expressed genes were identified, including 489 up-regulated and 293 down-regulated genes. Glutathione metabolism, detoxification response and energy metabolism were significantly enriched, revealing the potential toxic mechanism of haloxyfop-P-methyl to C. dehaani. These results provide a theoretical foundation for further research on haloxyfop-P-methyl toxicity to crustaceans.

Transcriptome sequencing reveals improved ammonia nitrogen tolerance in Zebra II strain of the Manila clam Ruditapes philippinarum

In this research, we identified genes associated with ammonia nitrogen (TAN) stress response and resistance in juveniles of the Zebra II strain and a wild population of the Manila clam Ruditapes philippinarum. Both groups were subjected to a 96 h acute toxicity test using TAN concentrations of 17.617 ± 0.634 and 16.670 ± 0.7 mg/l, respectively. We then collected samples, conducted transcriptome sequencing and screened the sequences for differentially expressed genes (DEGs) related to TAN stress response. We identified 2908 and 2861 DEGs in the Zebra II and wild clam groups, respectively, and the two groups had 626 DEGs in common. The verified DEGs had less of a detoxification effect in the wild population than that in the Zebra II group. Gene Ontology database analysis showed that Zebra II juveniles were mainly enriched in protein phosphorylation, purine nucleoside binding, and kinase activity, whereas the wild population juveniles were primarily enriched in oxidases activity, organic acid metabolic processes, and extracellular regions. Kyoto Encyclopedia of Genes and Genomes pathway analysis mainly highlighted aminoacyl tRNA biosynthesis in Zebra II juveniles and sphingolipid metabolism, FOXO signaling, biosynthesis of aminoacyl tRNA, and other pathways in the wild population. These results show that the toxic effect of TAN on the Manila clam is related to a variety of pathways, which are mainly related to immune response, inflammatory response, metabolic pathways, and nerve conduction. This study provides basic data and theoretical reference for revealing the molecular regulation mechanism of the improved TAN tolerance of Zebra II strain as compared with the wild population of Ruditapes philippinarum.

Water parameters correlated with the zootechnical performance of shrimp Litopenaeus vannamei grown in oligohaline waters

The present study aimed to correlate the influence of water quality, cultivation time, area, and density of ponds on the zootechnical performance of shrimp Litopenaeus vannamei in oligohaline waters. It was demonstrated that, under the conditions of this research, better control of temperature, pH and water alkalinity can be employed. Ammonia levels were within the normal range and correlated positively with the growth rate (ρ = 0.69859) and production (ρ = 0.66362) of the ponds. There was also a positive correlation between cultivation time and pond density with shrimp weight (ρ = 0.75305 and 0.68933) and pond productivity (ρ = 0.74763 and 0.79367, respectively). Negative correlations were observed between: I) pH with shrimp survival (ρ = -0.73238) and pond production (ρ = -0.68696); II) alkalinity and pond production (ρ = -0.66162). The results show that the cultivation of shrimp L. vannamei in oligohaline waters is viable and there is potential for increased productivity associated with better hydrological monitoring and use of higher density and cultivation time by some producers.

Acute ammonia stress-induced oxidative and heat shock responses modulated by transcription factors in Litopenaeus vannamei

The present study aimed to examine the effects of short-term exposure to ammonia on stress and oxidative responses in shrimp (Litopenaeus vannamei) and to determine whether the antioxidant system related to the regulatory role of transcription factors and stress proteins was activated. Shrimp were exposed ammonia-N at four concentrations: 0 (control), 5, 10, and 15 mg/L, for 48 h. The hepatopancreas was sampled to measure the levels of glutathione (GSH), malondialdehyde (MDA), nitric oxide (NO); the activities of superoxide dismutase (SOD), catalase (CAT), nitric oxide synthase (NOS); and the expression levels of GSH-px (encoding glutathione peroxidase), GST (encoding glutathione-S-transferase), HSP70 (encoding heat shock protein 70), HSP90 (encoding heat shock protein 90), p53, RELISH, and AKIRIN. We observed that exposure to a high ammonia content increased the abundance of oxidative factors (MDA, CAT, SOD, NOS, and NO), reduced the levels of GSH, and upregulated the mRNA expression levels of antioxidant genes (GSH-px and GST), stress-related genes (HSP70 and HSP90), and transcription factor genes (p53, RELISH, and AKIRIN). These results indicated that ammonia induced oxidative stress and inflammation. Both enzymatic and nonenzymatic antioxidant defense systems are involved, which might be regulated by HSPs, as well as certain transcription factors, such as p53 and nuclear factor kappa B (NF-κB), thus mounting an adaptive response to help rebalance redox homoeostasis.

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

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

Single-Cell Sequencing Reveals Types of Hepatopancreatic Cells and Haemocytes in Black Tiger Shrimp (Penaeus monodon) and Their Molecular Responses to Ammonia Stress

The cell types and developmental trajectories of shrimp cells based on the transcriptional level have not been established, and gene expression profile and function at the single-cell level is unclear. We aimed to use scRNA-seq to construct a single-cell resolution transcriptional map of hepatopancreas and haemocytes in shrimp to analyse the molecular mechanisms of the immune response to ammonia nitrogen stress. In the present study, seven cell clusters were successfully identified in each of the two tissues (haemocytes, Hem1-7; hepatopancreas, Hep1-7) based on specifically-expressed marker genes. The developmental starting points of haemocytes and hepatopancreatic cells were Hem2 and Hep1, respectively. We propose that Hem2 has oligopotent potential as the initiation site for haemocyte development and that Hem4 and Hem5, located at the end of development, are the most mature immune cell types in haemocytes. Hep5 and Hep6 were the developing terminal cells of hepatopancreas. The antioxidant system and proPO system of shrimp were activated under ammonia nitrogen stress. A large number of DEGs were involved in oxidative stress, detoxification metabolism, and immune defence. In particular, important response genes such as AMPs, proPO, and GST were not only marker genes for identifying cell groups but also played an important role in shrimp cell differentiation and functional plasticity. By successfully applying 10× Genomics based scRNA-seq to the study of shrimp, the single-cell transcriptional profiles of hepatopancreatic cells and haemocytes of shrimp innate immune responses under ammonia stress were constructed for the first time. This atlas of invertebrate hepatopancreatic cells and haemocytes at single-cell resolution identifies molecular events that underpin shrimp innate immune system responses to stress.

TBC domain family 7-like enhances the tolerance of Penaeus vannamei to ammonia nitrogen by the up-regulation of autophagy

TBC domain family 7 (TBC1D7) is one of the subunits of tuberous sclerosis complex (TSC) and an important regulator of autophagosome biogenesis. However, the function of TBC1D7 is not fully understood in crustaceans. In the present study, TBC1D7 was identified from Penaeus vannamei. The complete coding sequence of PvTBC1D7 was of 960 bp encoding a predicted polypeptide of 319 amino acids with one conserved TBC domain, which shared high similarity with TBC1D7 of that other species. The mRNA of PvTBC1D7 was highly expressed in hemocyte and hepatopancreas, and the PvTBC1D7 protein was localized specifically in the cytoplasm of hemocyte of shrimp. Besides, PvTBC1D7 was co-localized with PvTSC1 in the cytoplasm of shrimp, indicating that there might existed a binding relationship between PvTBC1D7 and PvTSC1. During the ammonia nitrogen stress, the mRNA transcripts of PvTBC1D7 were significantly upregulated in hemocyte, hepatopancreas, and gill. Functionally, overexpression of PvTBC1D7 in vitro restored the inhibition to autophagy caused by chloroquine (CLQ) and increased the autophagy level, while the silencing of PvTBC1D7 could inhibit the autophagy. More importantly, after interfering with PvTBC1D7, the autophagy level decreased significantly both in hepatopancreas and hemocyte of P. vannamei, the mRNA expression of PvmTOR was increased remarkably with the significantly decrease of autophagy-related genes (PvATG12 and PvATG14). And the reduction of PvTBC1D7 remarkably exacerbated the damage of hepatopancreas, increased the accumulation of ROS, and reduced the survival proportion of shrimp under ammonia nitrogen stress. Altogether, these results indicated that PvTBC1D7 might positively regulate the autophagy by stabilizing the negative regulation of mTOR by TSC complex, reduce the oxidative stress damage and improve shrimp ammonia nitrogen tolerance.

Identification of Candidate Genes Associated With Hypoxia Tolerance in Trachinotus blochii Using Bulked Segregant Analysis and RNA-Seq

Golden Pompano (Trachinotus blochii) has rapidly developed into the one of the main valuable fish species in Chinese marine aquaculture. Due to its rapid growth, active metabolism, and high oxygen consumption, hypoxia will increase its mortality and cause serious economic losses. We constructed two experimental groups of fish with different degrees of tolerance to hypoxia, used BSR-Seq analysis based on genome and genetic linkage groups to locate SNPs and genes that were related to the differences in hypoxia tolerance. The results showed that hypoxia tolerance SNPs of golden pompano may be jointly determined by multiple linkage groups, especially linkage groups 18 and 22. There were 768 and 348 candidate genes located in the candidate regions of the brain and liver, respectively. These genes were mainly involved in anaerobic energy metabolism, stress response, immune response, waste discharge, and cell death. The prostaglandin-endoperoxide synthase 2 (PTGS2) on LG8, which is involved in the metabolism of arachidonic acid, has a G/A nonsynonymous mutation at position 20641628, and the encoded amino acid was changed from hydrophobic aspartic acid to asparaginate. The specific pathway of the RIG-I-like receptor signaling pathway in the liver may mediate the metabolic system and the immune system, linking glucose metabolism with immune regulation. The death of the hypoxia-intolerant group may be due to the accumulation of lactic acid caused by the activation of anaerobic glycolysis during the early stage of hypoxia stress, and the activation of type I interferon was inhibited, which resulted in decreased immunity. Among the genes involved in the RIG-I-like receptor signaling pathway, the CYLD Lysine 63 Deubiquitinase (CYLD) located on LG16 had a G/T nonsynonymous mutation at position 13629651, and the encoded amino acid was changed from alanine acid to valine. The interferon induced with helicase C domain 1 (Ifih1) located on LG18 has a G/C nonsynonymous mutation at position 16153700, and the encoded hydrophilic glycine was changed to hydrophobic alanine. Our findings suggest these SNPs may assist in the molecular breeding of hypoxia-tolerant golden pompano, and speculate that the balance of glucose and lipid metabolism plays a key role in Trachinotus blochii under acute hypoxia.

Integrated physiological, transcriptome and metabolome analyses of the hepatopancreas of the female swimming crab Portunus trituberculatus under ammonia exposure

Ammonia is a common environmental pollutant in aquatic ecosystem and is also a significant concern in closed aquaculture systems. The threat of ammonia has been increasing with rising anthropogenic activities including intensified aquaculture. In this study, we aimed to investigate ammonia toxicity and metabolism mechanisms in the hepatopancreas, a major organ for Vitellogenin (Vtg) synthesis and defending against ammonia stress, of female swimming crab Portunus trituberculatus which is an important fishery and aquaculture species, by integrating physiological, transcriptome and metabolome analyses. The results revealed that ammonia exposure (10 mg/L, an environmentally relevant concentration) resulted in a remarkable reduction in vtg expression and depression of multiple signaling pathways for reproductive regulators including methyl farnesoate, ecdysone and neuroparsin, demonstrating for the first time that ammonia impairs swimming crab female reproduction. In addition, a number of important genes and metabolites in glycolysis, the Krebs cycle, fatty acid β-oxidation and synthesis were significantly downregulated, indicating that changes in ammonia levels lead to a general depression of energy metabolism in hepatopancreas. After ammonia exposure, an increased level of urea and a reduction of amino acid catabolism were observed in hepatopancreas, suggesting that urea cycle was utilized to biotransform ammonia, and amino acid catabolism was decreased to reduce endogenous ammonia generation. Furthermore, antioxidant systems were altered following ammonia exposure, which was accompanied by proteins and lipid oxidations, as well as cellular apoptosis. These results indicate that ammonia leads to metabolic suppression, oxidative stress and apoptosis in P. trituberculatus hepatopancreas. The findings improve the understanding for the mechanisms of ammonia toxicity and metabolism in P. trituberculatus, and provide valuable information for assessing potential ecological risk of environmental ammonia and improving aquaculture management.

Immune defense, detoxification, and metabolic changes in juvenile Eriocheir sinensis exposed to acute ammonia

Ammonia-N accumulation in the rice-crab co-culture system may have negative effects on the health of juvenile Eriocheir sinensis. In this study, physiological, transcriptomic, and metabolomic analyses were performed to explore the toxic responses in the hepatopancreas of juvenile E. sinensis exposed to 0, 0.75, and 2.99 mmol/L total ammonia-N for 24 h. We observed that the content of most amino acids and glycogen was significantly decreased after ammonia exposure. Acid phosphatase and alkaline phosphatase activities showed marginally increased trends after low ammonia exposure. Transcriptomic analysis indicated that immune defense, detoxification, and metabolic pathways were altered. Metabolomic analysis revealed that ammonia exposure affected energy metabolism and nucleotide metabolism. The combination of transcriptomic and metabolomic analyses revealed that the tricarboxylic acid cycle and amino acid consumption were enhanced for additional energy supply to cope with ammonia stress. Ammonia stress activated the immune defense system in juvenile E. sinensis. Moreover, the upregulation of detoxification genes and the acceleration of glycogen degradation for glucose supply are important adaptive mechanisms in response to high ammonia stress. Notably, ammonia stress may affect the nervous system of juvenile E. sinensis. Thus, our data provide a better understanding of the defensive mechanisms of E. sinensis against ammonia toxicity.

Ammonia stress influences intestinal histomorphology, immune status and microbiota of Chinese striped-neck turtle (Mauremys sinensis)

Ammonia is one of major pollutants in aquatic environment that induces severe stress and toxicity to organisms in aquatic system. The intestine acts a major defense line that protects living organisms from biotic and abiotic stresses. In the current study, we examined the effects of ammonia on intestinal histomorphology, transcriptional levels of intestinal barrier functioning genes and intestinal microbiota of Chinese striped-neck turtle (Mauremys sinensis). Thus, the turtles were placed in water with addition of ammonia at 0 (control), 100, 200 mg L^-1 for 30 days. Our findings showed that ammonia reduced the villus length and induced the inflammatory cells appearance. In addition, the epithelial tight junction genes, claudin and zonola occludin significantly downregulated in ammonia exposed groups as compared to control group (P < 0.05). Similarly, the mRNA expression levels of MUC-2 gene also significantly decreased in ammonia treated groups (P < 0.05). However, the expression levels of intestinal immune related genes such as IL-10, IL-12, TGF-β1, TNF-α and IFN-γ significantly increased (P < 0.05). Furthermore, ammonia changed gut microbial diversity variedly. At the phylum levels, Firmicutes increased, whereas Bacteroidota, Desulfobacterota and Synergistota decreased significantly. Likewise, Lachnospiraceae, Bacteroides, Eubacteriaceae, Desulfovibrio, Muribaculaceae, Bilophila, Cloacibacillus, Christensenellaceae, Ruminococcus and Parabacteroides decreased while, Romboutsia and Turicibacter increased in ammonia exposed groups. In conclusion, ammonia at 100 and 200 mg L^-1 could alter the intestinal barrier function and change the composition of intestinal microbiota, leading to bad health status in M. sinensis.

Transcriptome analysis to elucidate the toxicity mechanisms of fenvalerate, sulfide gatifloxacin, and ridomil on the hepatopancreas of Procambarus clarkii

Most antibiotics, insecticides, and other chemicals used in agricultural and fishery production tend to persist in the environment. Fenvalerate, sulfide gatifloxacin, and ridomil are widely used in aquaculture as antibacterial, antifungal, and antiparasitic drugs; however, their toxicity mechanism remains unclear. Thus, we herein analyzed the effects of these three drugs on the hepatopancreas of Procambarus clarkii at the transcriptome level. Twelve normalized cDNA libraries were constructed using RNA extracted from P. clarkii after treatment with fenvalerate, sulfide gatifloxacin, or ridomil and from an untreated control group, followed by Kyoto Encyclopedia of Genes and Genomes pathway analysis. In the control vs fenvalerate and control vs sulfide gatifloxacin groups, 14 and seven pathways were significantly enriched, respectively. Further, the effects of fenvalerate and sulfide gatifloxacin were similar on the hepatopancreas of P. clarkii. We also found that the expression level of genes encoding senescence marker protein-30 and arylsulfatase A was downregulated in the sulfide gatifloxacin group, indicating that sulfide gatifloxacin accelerated the apoptosis of hepatopancreatocytes. The expression level of major facilitator superfamily domain containing 10 was downregulated, implying that it interferes with the ability of the hepatopancreas to metabolize drugs. Interestingly, we found that Niemann pick type C1 and glucosylceramidase-β potentially interact with each other, consequently decreasing the antioxidant capacity of P. clarkii hepatopancreas. In the fenvalerate group, the downregulation of the expression level of xanthine dehydrogenase indicated that fenvalerate affected the immune system of P. clarkii; moreover, the upregulation of the expression level of pancreatitis-associated protein-2 and cathepsin C indicated that fenvalerate caused possible inflammatory pathological injury to P. clarkii hepatopancreas. In the ridomil group, no pathway was significantly enriched. In total, 21 genes showed significant differences in all three groups. To conclude, although there appears to be some overlap in the toxicity mechanisms of fenvalerate, sulfide gatifloxacin, and ridomil, further studies are warranted.

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei

The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components' significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities' structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction's bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp's gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

Analysis of transcriptome difference between rapid-growing and slow-growing in Penaeus vannamei

Penaeus vannamei is the principle cultured shrimp species in China. However, with the increase of culture density, the growth difference between individuals is also expanding. Here, we make use of RNA-seq to study the growth mechanisms of P. vannamei. After 120 days, we examined the transcriptomes of rapid-growing individuals (RG) and slow-growing individuals (SG). A total of 2116 and 176 differentially expressed genes (DEGs) were found in SG and RG, respectively. Moreover, the main DEGs are opsin, heat shock protein (HSP), actin, myosin, superoxide dismutase (SOD), cuticle protein, and chitinase. GO analysis further revealed that the DEGs were enriched in biological processes significantly, such as "sensory perception," "sensory perception of light stimulus," "response to stimulus," and "response to stress." Additionally, KEGG enrichment analysis showed that the DEGs were mainly enriched in "pentose and glucuronate interconversions," "amino sugar and nucleotide sugar metabolism," "glycophospholipid biosynthesis," and "glutathione metabolism." Interestingly, the upstream genes in the ecdysone signaling pathway, including molting inhibition hormone (MIH) and crustacean hyperglycemic hormone (CHH), did not differ significantly between RG and SG, which suggests that the cause for the inconsistent growth performance is due to the stress levels rather than the ecdysone signal pathway. In summary, this work provides data that will be useful for future studies on shrimp growth and development.

Effects of acute ammonia exposure on antioxidant and detoxification metabolism in clam Cyclina sinensis

To investigate the defensive strategies of clam Cyclina sinensis in response to environmental ammonia exposure, we investigate the 96 h median lethal concentration (LC₅₀-96 h) and the 96 h safe concentration (SC) of total ammonia nitrogen (TAN) for C. sinensis, and on the basis we examined glutamine synthetase (GS) activity, glutamine content, urea content and the antioxidant enzyme activities of super oxide dismutase (SOD) and catalase (CAT) in 96 h at three different levels of TAN as 0 (control), 73.94 (T1) and 227.04 mg/L (T2). Results showed that LC₅₀-96 h and SC for C. sinensis were 65.79 and 6.58 mg/L, respectively. The LC₅₀-96 h and SC of NH₃ were 1.70 and 0.17 mg/L, respectively. Ammonia exposure had significantly effects on SOD and CAT activities in the hepatopancreas tissue. Both the level of SOD activity and CAT activity increased with increasing concentration of TAN. No significant differences between T1 and T2 were found in GS activity from 3 h to 96 h after exposed to ammonia, whereas they were significantly higher than those in the control. Both the level of glutamine content in T1 and T2 increased significantly from 6 h to 24 h after exposed to ammonia and they were significantly higher than those in the control. There were no significantly differences were found in the level of urea concentration between T1 and T2 from 6 h to 96 h, while they were significantly higher those in the control. In conclusion, enhancing hepatopancreas antioxidant responses as well as converting ammonia into glutamine and urea worked in combination to allow C. sinensi to defend against acute ammonia exposure.

Comparative transcriptome reveals the response of oriental river prawn (Macrobrachium nipponense) to sulfide toxicity at molecular level

Aquatic environmental pollutants have various impacts on aquaculture. Specifically, sulfide has been established as being toxic to aquatic animals including the oriental river prawn Macrobrachium nipponense. In response, the hepatopancreas has been broadly studied, as it plays a pivotal role in arthropod nutrient digestion and absorption, energy supply, and organ development as well as in crustacean immunity. However, the underlying molecular mechanisms of hepatopancreas's response to sulfide toxicity are still poorly understand. Herein, we used Nova-seq 6000 platform to conduct a comparative transcriptome analysis of gene expression profiles in the hepatopancreas of M. nipponense, while it was under the influence of a semi-lethal sulfide concentration (3.20 mg/L at 48 h). A total of 139 million raw reads were obtained, in which 67,602 transcripts were clustered into 37,041 unigenes for further analysis. After constant sulfide exposure for 48 h, 235 differentially expressed genes, i.e., DEGs (151 up-regulated and 84 down-regulated) were identified in the sulfide treatment group (TGHP) compared with the control group (CGHP). We used GO and KEGG databases to annotate all the DEGs into 1180 functions and 123 pathways, respectively. The metabolic pathways included proximal tubule bicarbonate reclamation, sulfur metabolism, glycolysis and gluconeogenesis, and the TCA cycle; while immune-related pathways contained Ras, Rap1, focal adhesion and platelet activation. Additionally, apoptosis-involved pathways e.g., lysosome, also exhibited remarkable alteration in the presence of sulfide stress. Notably, responses to external stimuli and detoxification genes- such as GSKIP, CRT2, APOD, TRET1, CYP4C3 and HR39- were significantly altered by the sulfide stress, indicating that significant toxicity was transferred through energy metabolism, growth, osmoregulatory processes and immunity. Finally, we demonstrated that in the present of sulfide stress, M. nipponense altered the expression of detoxification- and extracellular stimulation-related genes, and displayed positive resistance via tight junction activation and lysosome pathways. The results of these novel experiments shed light on the hepatopancreas's molecular response to sulfide stress resistance and the corresponding adaptation mechanism; and enable us to identify several potential biomarkers for further studies.

Full-length transcriptome sequences of ridgetail white prawn Exopalaemon carinicauda provide insight into gene expression dynamics during thermal stress

Marine heat waves and extreme high temperature become more frequent and intense in these years, which affected the survival of aquaculture animals. The ridgetail white prawn Exopalaemon carinicauda is an important economic species in eastern China, which has remarkable thermal tolerance. However, there has been little study of its thermal-adaptation mechanisms due to the complex genetic structure and unknown genome. To better understand the molecular mechanisms of E. carinicauda to adapt to the changing temperature, a combination of Illumina-based short reads RNA-seq and single molecule real-time-based full-length transcriptome sequencing was used in this study. In total, 17,212 unigenes from high-quality transcripts of E. carinicauda were generated and 14,663 complete ORFs were detected with an average length of 1980 bp. In addition, the transcriptome profiles of E. carinicauda treated with 34 °C heat stress for 6 and 24 h were analyzed. These differentially expressed genes were primarily enriched in oxidation-reduction process (Gene Ontology enrichment, GO) and the pathways of starch and sucrose metabolism (Kyoto Encyclopedia of Genes and Genomes enrichment, KEGG) after 6 h thermal stress, which indicated that E. carinicauda was suffering the attack by reactive oxygen species. After 24 h thermal stress, these differentially expressed genes were enriched in the pathway of lysosome, glycine, serine and threonine metabolism, fatty acid metabolism (KEGG), which indicated the oxidative stress was decreased. Interestingly, 40 genes for hemocyanin were found to be downregulated after 6 h heat stress, which indicated that the immunocompetence of E. carinicauda decreased after short term thermal stress (6 h). After 24 h thermal stress, E. carinicauda showed transcriptional adaptation to high temperature by upregulating of 11 genes encoding molecular chaperones, including HSP40 and HSP90 which were firstly reported to be related to thermal stress in E. carinicauda. These results promote a better understanding of the thermal-adaptation mechanism of E. carinicauda.

Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

Background

Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available.

Results

In this study, we constructed a high-density genetic map of the Pacific white shrimp (Litopenaeus vannamei) using specific length amplified fragment sequencing (SLAF-seq). The constructed genetic map contained 17,338 polymorphic markers spanning 44 linkage groups, with a total distance of 6360.12 centimorgans (cM) and an average distance of 0.37 cM. Using this genetic map, we identified a quantitative trait locus (QTL) that explained 7.41–8.46% of the phenotypic variance in L. vannamei survival time under acute ammonia stress. We then sequenced the transcriptomes of the most ammonia-tolerant and the most ammonia-sensitive individuals from each of four genetically distinct L. vannamei families. We found that 7546 genes were differentially expressed between the ammonia-tolerant and ammonia-sensitive individuals. Using QTL analysis and the transcriptomes, we identified one candidate gene (annotated as an ATP synthase g subunit) associated with ammonia tolerance.

Conclusions

In this study, we constructed a high-density genetic map of L. vannamei and identified a QTL for ammonia tolerance. By combining QTL and transcriptome analyses, we identified a candidate gene associated with ammonia tolerance. Our work provides the basis for future genetic studies focused on molecular marker-assisted selective breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07254-x.

Innate immune function of serine/threonine-protein kinase from Macrobrachium rosenbergii in response to host-pathogen interactions

The occurrences of multiple drug-resistant strains have been relentlessly increasing in recent years. The aquaculture industry has encountered major disease outbreaks and crucially affected by this situation. The usage of non-specific chemicals and antibiotics expedites the stimulation of resistant strains. Triggering the natural defense mechanism would provide an effective and safest way of protecting the host system. Hence, we have investigated the innate immune function of serine/threonine-protein kinase (STPK) in Macrobrachium rosenbergii (Mr). The in-silico protein analysis resulted in the identification of cationic antimicrobial peptide, MrSL-19, with interesting properties from STPK of M. rosenbergii. Antimicrobial assay, FACS and SEM analysis demonstrated that the peptide potentially inhibits Staphylococcus aureus by interacting with its membrane. The toxic study on MrSL-19 demonstrated that the peptide is not toxic against HEK293 cells as well as human erythrocytes. This investigation showed the significant innate immune property of an efficient cationic antimicrobial peptide, MrSL-19 of STPK from M. rosenbergii.

Hemocytes transcriptomes reveal metabolism changes and detoxification mechanisms in response to ammonia stress in Octopus minor

Ammonia is one of the major aquatic environmental pollutants that can bring detrimental effects to the growth and survival of aquatic organisms. However, the molecular mechanisms of ammonia toxicity and ammonia excretion in marine invertebrates especially mollusks are still poorly understood. Cephalopods are exclusively ammonotelic with high protein metabolism and ammonia excretion rate, making this taxonomic group an ideal specimen to explore the ammonia detoxification mechanism. In this study, comparative transcriptomes were employed to investigate the transcriptional changes of O. minor in responses to acute ammonia exposure. A total of 63,237 unigenes with an average length of 811 bp were discovered and 25,708 unigenes were successfully annotated. The transcription of 1845 genes were significantly changed after ammonia stress, including 315 up-regulated genes and 1530 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis based on differentially expressed genes (DEGs) revealed that 44 GO terms and 55 KEGG pathways were over-represented. Notably, a large number of genes involved in immune defense, citric acid (TCA) cycle, oxidative phosphorylation and amino acid metabolisms were significantly down-regulated, indicating the decelerated energy production and amino acid rate in response to acute ammonia stress. These results provide new insights into the potential molecular mechanism of ammonia detoxification on transcriptomic level and will facilitate further mechanism studies on mollusks.

Full-length transcriptome and long non-coding RNA profiling of whiteleg shrimp Penaeus vannamei hemocytes in response to Spiroplasma eriocheiris infection

Spiroplasma eriocheiris (S. eriocheiris) infection causes a significant economic loss in Penaeus vannamei (P. vannamei) culture industry. However, the response of P. vannamei hemocytes to S. eriocheiris infection has not been extensively studied. In this study, we conducted full-length transcriptome and long non-coding RNA (lncRNA) analyses of P. vannamei hemocytes by a challenge test with S. eriocheiris. Following assembly and annotation, there were 8077 high-quality unigenes. A total of 1168 differentially expressed genes (DEGs) were obtained, including 792 up-regulated and 376 down-regulated genes by differential expression analysis. Gene ontology (GO) enrichment analysis showed that the up-regulated DEGs were mainly clustered into immune system process, defense response, cell cycle and organelle organization. On the other hand, the down-regulated DEGs included that genes that were mainly clustered into metabolic processes related to organic compounds, metabolic process and cellular metabolic process. Protein-protein interaction (PPI) network analysis of DEGs indicated that the pivotal gene interactions were connected to stress response, immune system process and cell cycle. The lncRNA analysis identified multiple lncRNAs, which were highly co-expressed with the immune-related genes, such as lncRNA transcript-12631 and transcript-12631, suggesting that lncRNAs may be involved in the regulation of immune defense in shrimp hemocytes. Additionally, 20 hub unigenes and putative lncRNAs related to immune system were validated by quantitative real-time PCR (qRT-PCR), validating the reliability of RNA-Seq. This study revealed a close connection between the immune and metabolic systems of S. eriocheiris infected P. vannamei.

A SNP of the hemocyanin gene (LvHc) is a marker for high growth and ammonia-tolerance in Pacific white shrimp Litopenaeus vannamei

Expression levels of hemocyanin (LvHc), activating transcription factor 4 (LvAtf4), glutathione S-transferase (LvGst), caspase 2 (LvCasp2) and anti-lipopolysaccharide factor (LvAlf) were examined in the hepatopancreas of Pacific white shrimp Litopenaeus vannamei juveniles exposed to a lethal concentration of ammonia-N (32.15 mg/l). The expression levels of all transcripts except LvAlf were significantly greater (P < 0.05) in tolerant shrimp (Lv-AT; N = 30) that survived up to 72 h post treatment (hpt) than in susceptible shrimp (Lv-AS24 and Lv-AS72; N = 45 and 15), that died within 24 h or between 24 and 72 hpt, respectively. Subsequently, effects of non-lethal concentrations of ammonia-N (control, 10 and 20 mg/l) on the expression of LvHc in juvenile shrimp were examined. Compared to the control, expression levels of LvHc transcripts in hemocytes and the hepatopancreas of tested shrimp changed after exposure to ammonia-N. One SNP (C > T₅₄₅) was found in the LvHc₃₂₂ gene segment. Real-time PCR amplification of specific alleles (real-time PASA) was developed for detection of C > T₅₄₅ genotypes. Juveniles in the lethal exposure test that carried a C/T₅₄₅ genotype showed a greater average body weight and total length (8.46 ± 0.36 g and 10.05 ± 0.16 cm) than those with a C/C₅₄₅ genotype (7.48 ± 0.31 g and 9.60 ± 0.13 cm) (P < 0.05). Similar results were found in the second generation (G2) of a growth-improved stock (3 and 4 families of BIOTEC-G2-L1 and BIOTEC-G2-L2) and in commercially farmed shrimp (2 groups). Accordingly, expression levels and SNP of LvHc can serve as markers for selection high growth performance in ammonia-tolerant L. vannamei.

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci for Nitrite Tolerance in the Pacific White Shrimp (Litopenaeus vannamei)

Nitrite is a major environmental toxin in aquaculture systems that disrupts multiple physiological functions in aquatic animals. Although nitrite tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. In this study, we constructed a high-density genetic map of Litopenaeus vannamei with 17,242 single nucleotide polymorphism markers spanning 6,828.06 centimorgans (cM), with an average distance of 0.4 cM between adjacent markers on 44 linkage groups (LGs). Using this genetic map, we identified two markers associated with nitrite tolerance. We then sequenced the transcriptomes of the most nitrite-tolerant and nitrite-sensitive individuals from each of four genetically distinct L. vannamei families (LV-I–4). We found 2,002, 1,983, 1,954, and 1,867 differentially expressed genes in families LV-1, LV-2, LV-3, and LV-4, respectively. By integrating QTL and transcriptomics analyses, we identified a candidate gene associated with nitrite tolerance. This gene was annotated as solute carrier family 26 member 6 (SLC26A6). RNA interference (RNAi) analysis demonstrated that SLC26A6 was critical for nitrite tolerance in L. vannamei. The present study increases our understanding of the molecular mechanisms underlying nitrite tolerance in shrimp and provides a basis for molecular-marker-assisted shrimp breeding.

The krüppel-like factor of Penaeus vannamei negatively regulates transcription of the small subunit hemocyanin gene as part of shrimp immune response

Hemocyanin is a multifunctional respiratory glycoprotein, which has also been implicated in other biological functions in shrimp. Moreover, recent studies have revealed that hemocyanin is also involved in a broad range of immune-related activities in shrimp. However, in spite of the considerable interest in unraveling the reasons behind the multiple immune-related functions of hemocyanin, little is known about its transcriptional regulation. Here, DNA pull-down and Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) analyses were used to isolate and identify the putative transcription factor(s) that are involved in the transcriptional regulation of the small subunit hemocyanin gene of Penaeus vannamei (PvHMCs). Krüppel-like factor (designated PvKruppel), a zinc finger transcription factor homolog in P. vannamei, was identified among the putative transcription factors, while bioinformatics analysis revealed the presence of Krüppel-like factor binding site (KLF motif) on the core promoter region of PvHMCs. Mutational analysis and electrophoretic mobility shift assay (EMSA) confirmed that PvKruppel could bind to the KLF motif on the core promoter region of PvHMCs. Moreover, in response to lipopolysaccharide (LPS), Vibrio parahaemolyticus and white spot syndrome virus (WSSV) challenge, transcript levels of PvKruppel and PvHMCs were negatively correlated. Furthermore, overexpression of PvKruppel significantly reduced the promoter activity of PvHMCs, while PvKruppel knockdown by RNA interference or lipopolysaccharides (LPS) stimulation resulted in a significant increase in the transcript level of PvHMCs. Taken together, our present study provides mechanistic insights into the transcriptional regulation of PvHMCs by PvKruppel during shrimp immune response to pathogens.

How do abiotic environmental conditions influence shrimp susceptibility to disease? A critical analysis focussed on White Spot Disease

White Spot Syndrome Virus (WSSV) causes White Spot Disease (WSD) and is historically the most devastating disease in the shrimp industry. Global losses from this disease have previously exceeded $3 bn annually, having a major impact on a global industry worth US$19 bn per annum. Shrimp are cultured predominantly in enclosed ponds that are subject to considerable fluctuations in abiotic conditions and WSD outbreaks are increasingly linked to periods of extreme weather, which may cause major fluctuations in pond culture conditions. Combined with the intensity of production in these systems, the resulting suboptimal physicochemical conditions have a major bearing on the susceptibility of shrimp to infection and disease. Current knowledge indicates that pond temperature and salinity are major factors determining outbreak severity. WSSV appears to be most virulent in water temperatures between 25 and 28 °C and salinities far removed from the isoosmotic point of shrimp. Elevated temperatures (>30 °C) may protect against WSD, depending on the stage of infection, however the mechanisms mediating this effect have not been well established. Other factors relating to water quality that may play key roles in determining outbreak severity include dissolved oxygen concentration, nitrogenous compound concentration, partial pressure of carbon dioxide and pH, but data on their impacts on WSSV susceptibility in cultured shrimps is scarce. This illustrates a major research gap in our understanding of the influence of environmental conditions on disease. For example, it is not clear whether temperature manipulations can be used effectively to prevent or mitigate WSD in cultured shrimp. Therefore, developing our understanding of the impact of environmental conditions on shrimp susceptibility to WSSV may provide insight for WSD mitigation when, even after decades of research, there is no effective practical prophylaxis or treatment.

Transcriptomic analysis reveals different responses to ammonia stress and subsequent recovery between Coilia nasus larvae and juveniles

Excessive ammonia triggered negative effects on aquatic animals' health, growth, and mass death, especially at different developmental periods. However, the underlying responses to ammonia stress in fish larvae and juveniles were much less explored. Transcriptomic analysis of Coilia nasus larvae and juveniles treated with ammonia stress and subsequent recovery in freshwater were performed. Total 958,213,132 clean reads were obtained. A total of 234,830 unigenes with an average length of 1397 bp and N50 value 2521 bp were assembled. 831 and 952 DEGs were identified in C. nasus larvae and juveniles, respectively. Transcriptomic analysis revealed that genes associated with purine metabolism, immune, inflammation, epigenetic modification, and nerve conduction presented different expression trends between C. nasus larvae and juveniles. Other genes related to purine metabolism (XDH) and epigenetic modifications (DNMT1, DNMT3A, and DNMT3B) detected by RT-qPCR also displayed different expression trends. These results indicated that ammonia detoxify strategies and gene regulation patterns were different in C. nasus larvae and juveniles. Higher TNF-α, ILF-2, and ILF-3 expression and reduced LZM, AKP, and ACP activities suggested that inflammation and declined immunity were triggered by ammonia stress. Additionally, nervous conduction was severely affected under ammonia stress in C. nasus juveniles. Furthermore, recovery in freshwater had positive effects on nervous conduction. However, it was worth noting that reduced immunity and inflammation were still existed after recovery in freshwater. In conclusion, our study would be beneficial to reveal the different responses to ammonia stress between larvae and juveniles.

Transcriptomic response to three osmotic stresses in gills of hybrid tilapia (Oreochromis mossambicus female × O. urolepis hornorum male)

Background

Osmotic stress is a widespread phenomenon in aquatic animal. The ability to cope with salinity stress and alkaline stress is quite important for the survival of aquatic species under natural conditions. Tilapia is an important commercial euryhaline fish species. What’s more tilapia is a good experimental material for osmotic stress regulation research, but the molecular regulation mechanism underlying different osmotic pressure of tilapia is still unexplored.

Results

To elucidate the osmoregulation strategy behind its hyper salinity, alkalinity and salinity-alkalinity stress of tilapia, the transcriptomes of gills in hybrid tilapia (Oreochromis mossambicus ♀ × O. urolepis hornorum ♂) under salinity stress (S: 25‰), alkalinity stress(A: 4‰) and salinity-alkalinity stress (SA: S: 15‰, A: 4‰) were sequenced using deep-sequencing platform Illumina/HiSeq-2000 and differential expression genes (DEGs) were identified. A total of 1958, 1472 and 1315 upregulated and 1824, 1940 and 1735 downregulated genes (P-value < 0.05) were identified in the salt stress, alkali stress and saline-alkali stress groups, respectively, compared with those in the control group. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted in the significant different expression genes. In all significant DEGs, some of the typical genes involved in osmoregulation, including carbonic anhydrase (CA), calcium/calmodulin-dependent protein kinase (CaM kinase) II (CAMK2), aquaporin-1(AQP1), sodium bicarbonate cotransporter (SLC4A4/NBC1), chloride channel 2(CLCN2), sodium/potassium/chloride transporter (SLC12A2 / NKCC1) and other osmoregulation genes were also identified. RNA-seq results were validated with quantitative real-time PCR (qPCR), the 17 random selected genes showed a consistent direction in both RNA-Seq and qPCR analysis, demonstrated that the results of RNA-seq were reliable.

Conclusions

The present results would be helpful to elucidate the osmoregulation mechanism of aquatic animals adapting to saline-alkali challenge. This study provides a global overview of gene expression patterns and pathways that related to osmoregulation in hybrid tilapia, and could contribute to a better understanding of the molecular regulation mechanism in different osmotic stresses.

Effects of ammonia stress on the hemocytes of the Pacific white shrimp Litopenaeus vannamei

Ammonia is an important environmental stress factor in aquaculture. Long-term ammonia stress could affect the normal growth, and also increase the risk for the occurrence of various diseases. In order to learn the mechanism that ammonia caused the outbreak of the shrimp disease, transcriptomics and metabolomics approaches were used to analyze the differential expressions of the genes in hemocytes and different metabolites in the serum of the Pacific white shrimp Litopenaeus vannamei under ammonia exposure. Transcriptional analysis showed that 17 cell apoptosis related genes, seven phagocytosis related genes, 10 immunity related genes and seven cell cycle and lipid metabolism related genes showed differential expressions after ammonia exposure. Metabolomics analysis on the serum showed that 25 differential metabolites were identified in positive and negative ion patterns. They are involved in purine metabolism, amino acids metabolism and lipid metabolism. Injection of two up-regulated metabolites triethanolamine and oxypurinol to normal shrimp could induce apoptosis in normal shrimp. The total hemocytes counts in shrimp showed a significant decrease and the apoptotic cell ratio increased significantly under ammonia exposure. These results suggested that ammonia exposure increased the apoptosis of hemocytes, which affected the immunity of shrimp, and thus caused susceptibility to pathogenic infection. These data will help us understand the mechanism of ammonia stress leading to the immunity decline of shrimp.

Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge

To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.

Stress response and tolerance mechanisms of ammonia exposure based on transcriptomics and metabolomics in Litopenaeus vannamei

Ammonia, one of the major limiting environment factors in aquaculture, may pose a threat to the shrimp growth, reproduction and survival. In this study, to understand molecular differences of transcriptomic and metabolomic responses and investigate the tolerance mechanisms underlying ammonia stress in Litopenaeus vannamei, ammonia-tolerant family (LV-AT) and ammonia-sensitive family (LV-AS) of these two extreme families were exposed to high-concentration (NH₄Cl, 46 mg/L) ammonia for 24 h. The comparative transcriptome analysis between ammonia-treated and control (LV-C) groups revealed involvement of immune defense, cytoskeleton remodeling, antioxidative system and metabolic pathway in ammonia-stress response of L. vannamei. Likewise, metabolomics analysis showed that ammonia exposure could disturb amino acid metabolism, nucleotide metabolism and lipid metabolism, with metabolism related-genes changed according to RNA-seq analysis. The comparison of metabolite and transcript profiles between LV-AT and LV-AS indicated that LV-AT used the enhanced glycolysis and tricarboxylic acid (TCA) cycle strategies for energy supply and ammonia excretion to adapt high-concentration ammonia. Furthermore, some of genes involved in the detoxification and ammonia excretion were highly expressed in LV-AT. We speculate that the higher ability of ammonia excretion and detoxification and the accelerated energy metabolism for energy supplies might be the adaptive strategies for LV-AT relative to LV-AS after ammonia stress. Collectively, the combination of transcriptomics and metabolomics results will greatly contribute to incrementally understand the stress responses on ammonia exposure to L. vannamei and supply molecular level support for evaluating the environmental effects of ammonia on aquatic organisms. The results further constitute new sights on the potential molecular mechanisms of ammonia adaptive strategies in shrimps at the transcriptomics and metabolomics levels.

Transcriptome analysis of response mechanism to ammonia stress in Asian clam (Corbicula fluminea)

Corbicula fluminea is highly sensitive to ammonia, and its response mechanism to ammonia stress is unclear. In this study, C. fluminea was exposed to different levels of ammonia (control group, 10 mg/L, and 25 mg/L) for 24 h and 48 h. A comparative analysis of transcriptome sequencing (RNA-seq) of C. fluminea digestive gland showed that the expression of 6742 genes (11.54%) was significantly affected by ammonia stress. The TLR, NF-κB, FOXO, and apoptotic signaling pathways were involved in the regulation. The differential expression of 14 genes was confirmed by real-time PCR. In summary, the response mechanism of C. fluminea digestive gland under ammonia stress may be different from that of oxidative stress in marine vertebrates. Also, the NMDAR-mediated pathway may not be the main mechanism in the response to ammonia stress in C. fluminea. The present study is a preliminary study for further investigation into ammonia toxicity in shellfish.

C-type lectin response to bacterial infection and ammonia nitrogen stress in tiger shrimp (Penaeus monodon)

C-type lectins (CTLs) are pattern recognition receptors (PRRs) that are important in invertebrate innate immunity for the recognition and elimination of pathogens. Although they were reported in many shrimp, C-type lectins subfamily contain a large number of members with different functions that need to research in deep. In this present study, a new type of CTL, PmCL1 with 861 bp long full-length cDNA, that encodes a protein with 164-amino acid from a 495-bp open reading frame, was isolated and characterized from tiger shrimp (Penaeus monodon). The mRNA transcript of PmCL1 showed the highest expression in the hepatopancreas, whereas it was barely detected in the ovary. After the shrimp were stimulated by Vibrio harveyi and Vibrio anguillarum, PmCL1 expression in the hepatopancreas and gill was significantly upregulated. A carbohydrate-binding assay revealed the specificity of PmCL1 for pathogen-associated molecular patterns (PAMPs) that included peptidoglycan (PGN) and lipopolysaccharide (LPS), and saccharides that included d-glucose, galactosamine, α-lactose, treholose, and d-mannose. Recombinant PmCL1 agglutinated gram-positive (Staphylococcus aureus) and gram-negative bacteria (V. harveyi, V. anguillarum, Vibrio alginolyticus, Vibrio parahemolyticus, Vibrio vulnificus, and Aeromonas hydrophila) in the presence of calcium ions and enhanced the efficiency of clearing the invading bacteria. Collectively, our results suggested that PmCL1 might play an important role as a pattern recognition receptor (PRR) in the immune response towards pathogen infections, as well as the response towards ammonia nitrogen stress.

Insights into the molecular basis of immunosuppression and increasing pathogen infection severity of ammonia toxicity by transcriptome analysis in pacific white shrimp Litopenaeus vannamei

The high concentration of ammonia resulting from intensive culture system and environmental pollution could cause disease occurrence in shrimp, but little information is available on its molecular mechanisms. In this study, we performed comparative transcriptome analysis among WSSV-infected shrimp under ammonia stress (LAV), WSSV-infected shrimp under normal water (LV), and normal shrimp under ammonia stress (LA) groups to identify the key genes and pathways involved in immunosuppression and increasing pathogen infection severity caused by ammonia toxicity in Litopenaeus vannamei. Totally, 526 significantly differential expressed genes (DEGs) were identified in LAV group compared to LV and LA groups, among which 270 genes were lost expressed and 67 genes uniquely expressed in the LAV group. According to the public functional reports for the annotated DEGs, they potentially involved in the following functions: (1) accelerating pathogen adhesion, invasion and multiplication; (2) reducing the ability for pathogen defense and immune response; (3) inhibiting positive regulation of apoptotic and antioxidant defense for host homeostasis; (4) inhibiting transcription and protein transport; (5) and increasing protein methylation and ubiquitination, etc. A total of 13 pathways were obtained mainly involving in this process, which mainly led to the following changes: (1) increasing the immunosuppression, anemia, endocrine dysfunction, neurotoxic effect and neuroinvasion, atherosclerosis and thrombogenesis, blood-brain barrier penetration, thyroid disorder, necrosis, inflammation, and circadian disturbance; (2) reducing the ability of vascular remodeling, angiogenesis, cell survival, migration, apoptosis, and lymph transferred to blood stream; (3) leading to cell hypertrophy, cellular shape changes, and mesangial matrix expansion. The present results firstly supplied molecular mechanisms for the ammonia toxicity inhibiting the immune system and increasing pathogen infection severity in shrimp, which is a prerequisite for better understanding the pathogenesis caused by ammonia toxicity.

Comparative transcriptomic characterization of the eyestalk in Pacific white shrimp (Litopenaeus vannamei) during ovarian maturation

In crustaceans, some of fundamental regulatory processes related to a range of physiological functions, including ovarian maturation, molting, glucose homeostasis, osmoregulation, etc., occur in the organs of the eyestalk. Additionally, reproduction is regulated by neuropeptide hormones and other proteins released from secretory sites (X-organ/sinus gland, XO/SG) within the eyestalk. As unilateral eyestalk ablation was the most common method used to artificially induce ovarian maturation for farmed Litopenaeus vannamei, to better understand the reproductive regulation mechanism in L. vannamei, we have investigated the transcriptomes of the eyestalk during five ovary developmental stages with or without eyestalk ablation by high-throughput Illumina sequencing technology. The raw reads were assembled and clustered into 127,031 unigenes. Meanwhile, the differentially expressed genes (DEGs) between ovarian development stages were identified. We examined, through DEG enrichment analysis, eyestalk gene expression patterns for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, comparing natural to artificially induced ovarian maturation. We also identified a variety of transcripts that appear to be differentially expressed throughout ovarian maturation. These include transcripts that encode G-protein coupled receptors (GPCRs) and neuropeptides, such as the crustacean hyperglycemic hormone (CHH), molt-inhibiting hormone (MIH), and crustacean female sex hormone (CFSH). Furthermore, numerous exoskeleton formation-related genes were found to be down-regulated during ovarian maturation, including cuticle-like proteins, eclosion hormone (EH), and gastrolith-like proteins, of which the latter are the first reported in L. vannamei. Our work is the first reproduction-related investigation of L. vannamei focusing on the eyestalk at the whole transcriptome level. These findings provide novel insight into the function of the eyestalk in reproduction regulation.

Effect of dietary date seed meal as an alternative carbohydrate source on immune-related gene expression of Pacific white shrimp Penaeus vannamei

Current study aimed to examine the effect of dietary date seed meal (DSM) as an alternative carbohydrate ingredient on immune-related genes expression of Pacific white shrimp (Penaeus vannamei). A total number of 750 shrimp (4.0 ± 0.1 g) were randomly assigned into five experimental treatments, each with three replicates. Experimental diets contained 0, 50, 100, 150 and 230 g/kg DSM substituted for both wheat and rice flour. Shrimp were fed at a rate of 5% body weight three times daily and the mRNA expression of α2-macroglobulin (α2-M), lipopolysaccharide and beta-1,3-glucan-binding protein (LGBP), integrin β, and peroxinectin (PX) was studied on five shrimp per treatment after 8 weeks feeding trial. The results showed that replacement of DSM up to 100 g/kg in the diet of P. vannamei caused no significant changes in the expression of α2-M and integrin β, however both of these genes showed lower expression in shrimp fed diets containing 150 and 230 g/kg DSM compared to control group. Moreover, no significant differences were observed in the expression of PX and LGBP between shrimp fed diets containing different amounts of DSM and control group. These findings demonstrated that as an inexpensive source of carbohydrate, DSM could be substituted up to 100 g/kg for wheat and rice flour in the diet of farmed shrimp without suppressive effects on the immune status.

Effects of environmental stress on shrimp innate immunity and white spot syndrome virus infection

The shrimp aquaculture industry is plagued by disease. Due to the lack of deep understanding of the relationship between innate immune mechanism and environmental adaptation mechanism, it is difficult to prevent and control the diseases of shrimp. The shrimp innate immune system has received much recent attention, and the functions of the humoral immune response and the cellular immune response have been preliminarily characterized. The role of environmental stress in shrimp disease has also been investigated recently, attempting to clarify the interactions among the innate immune response, the environmental stress response, and disease. Both the innate immune response and the environmental stress response have a complex relationship with shrimp diseases. Although these systems are important safeguards, allowing shrimp to adapt to adverse environments and resist infection, some pathogens, such as white spot syndrome virus, hijack these host systems. As shrimp lack an adaptive immune system, immunization therapy cannot be used to prevent and control shrimp disease. However, shrimp diseases can be controlled using ecological techniques. These techniques, which are based on the innate immune response and the environmental stress response, significantly reduce the impact of shrimp diseases. The object of this review is to summarize the recent research on shrimp environmental adaptation mechanisms, innate immune response mechanisms, and the relationship between these systems. We also suggest some directions for future research.

Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress

Soil salinization erodes the farmlands and poses a serious threat to human life, reuse of the saline-alkali lands as cultivated resources becomes increasingly prominent. Pacific white shrimp (Litopenaeus vannamei) is an important farmed aquatic species for the development and utilization of the saline-alkali areas. However, little is known about the adaptation mechanism of this species in terms of high-pH stress. In the present study, a transcriptome analysis on the gill tissues of L. vannamei in response to high-pH stress (pH 9.3 ± 0.1) was conducted. After analyzing, the cyclic nucleotide gated channel-Ca2+ (CNGC-Ca2+) and patched 1 (Ptc1) were detected as the majority annotated components in the cAMP signaling pathway (KO04024), indicating that the CNGC-Ca2+ and Ptc1 might be the candidate components for transducing and maintaining the high-pH stress signals, respectively. The immunoglobulin superfamily (IgSF), heat shock protein (HSP), glutathione s-transferase (GST), prophenoloxidase/phenoloxidase (proPO/PO), superoxide dismutase (SOD), anti-lipopolysaccharide factor (ALF) and lipoprotein were discovered as the major transcribed immune factors in response to high-pH stress. To further detect hub regulation-genes, protein-protein interaction (PPI) networks were constructed; the genes/proteins "Polymerase (RNA) II (DNA directed) polypeptide A" (POLR2A), "Histone acetyltransferase p300" (EP300) and "Heat shock 70kDa protein 8" (HSPA8) were suggested as the top three hub regulation-genes in response to acute high-pH stress; the genes/proteins "Heat shock 70kDa protein 4" (HSPA4), "FBJ murine osteosarcoma viral oncogene homolog" (FOS) and "Nucleoporin 54kDa" (NUP54) were proposed as the top three hub regulation-genes involved in adapting endurance high-pH stress; the protein-interactions of "EP300-HSPA8" and "HSPA4-NUP54" were detected as the most important biological interactions in response to the high-pH stress; and the HSP70 family genes might play essential roles in the adaptation of the high-pH stress environment in L. vannamei. These findings provide the first insight into the molecular and immune basis of L. vannamei in terms of high-pH environments, and the construction of a PPI network might improve our understanding in revealing the hub regulation-genes in response to abiotic stress in shrimp species and might be beneficial for further studies.

Transcriptome reveals involvement of immune defense, oxidative imbalance, and apoptosis in ammonia-stress response of the black tiger shrimp (Penaeus monodon)

Ammonia is a major aquatic environmental pollutant that negatively impacts shrimp health and commercial productivity. However, we currently do not fully understand the underlying molecular mechanisms of ammonia stress in shrimp. We therefore performed transcriptomic analysis of hepatopancreas from black tiger shrimp (Penaeus monodon) treated with ammonia-stress. We obtained 146,410,174 and 115,241,048 clean reads for the control and treatment groups, respectively. A total of 64,475 unigenes with an average length of 1275 bp and a N50 value of 2158 bp were assembled. A comparative transcriptome analysis identified 3462 differentially expressed genes, 177 of which are highly homologous with known proteins in aquatic species. Most of these genes showing the expression changes were related to immune function. Some significantly down-regulated genes are involved in purine metabolism and other metabolic pathways, which suggests that purineolytic capacity is an ammonia detoxification process in P. monodon, and metabolic depression is a strategy to reduce shrimp exposure to ammonia. Additionally, ammonia stress altered the expression patterns of key apoptosis genes (Bcl-xL, PERK, caspase 7, and caspase 10), confirmed that ammonia-stress induce oxidative stress and eventually even apoptosis. We also found evidence for the involvement of antioxidant defense in response to oxidative imbalance, given the regulation of peroxiredoxin 1, SOD, and CAT under ammonia stress. In conclusion, our study clarifies shrimp defensive response to ammonia toxicity and should benefit efforts to breed more ammonia-tolerant varieties.

Proteomic Responses Under Cold Stress Reveal Unique Cold Tolerance Mechanisms in the Pacific White Shrimp (Litopenaeus vannamei)

The Pacific white shrimp (Litopenaeus vannamei), one of the most widely cultured shrimp species in the world, often suffers from cold stress. To understand the molecular mechanism of cold tolerance in Pacific white shrimp, we conducted a proteomic analysis on two contrasting shrimp cultivars, namely, cold-tolerant Guihai2 (GH2) and cold-sensitive Guihai1 (GH1), under normal temperature (28°C), under cold stress (16°C), and during recovery to 28°C. In total, 3,349 proteins were identified, among which 2,736 proteins were quantified. Based on gene ontology annotations, differentially expressed proteins largely belonged to biological processes, cellular components, and molecular functions. KEGG pathway annotations indicated that the main changes were observed in the lysosome, ribosomes, and oxidative phosphorylation. Subcellular localization analysis showed a significant increase in proteins present in cytosol, extracellular regions, and mitochondria. Combining enrichment-based clustering analysis and qRT-PCR analysis, we found that glutathione S-transferase, zinc proteinase, m7GpppX diphosphatase, AP2 transcription complex, and zinc-finger transcription factors played a major role in the cold stress response in Pacific white shrimp. Moreover, structure proteins, including different types of lectin and DAPPUDRAFT, were indispensable for cold stress tolerance of the Pacific white shrimp. Results indicate the molecular mechanisms of the Pacific white shrimp in response to cold stress and provide new insight into breeding new cultivars with increased cold tolerance.

Molecular characterization of putative neuropeptide, amine, diffusible gas and small molecule transmitter biosynthetic enzymes in the eyestalk ganglia of the American lobster, Homarus americanus

The American lobster, Homarus americanus, is a model for investigating the neuromodulatory control of physiology and behavior. Prior studies have shown that multiple classes of chemicals serve as locally released/circulating neuromodulators/neurotransmitters in this species. Interestingly, while many neuroactive compounds are known from Homarus, little work has focused on identifying/characterizing the enzymes responsible for their biosynthesis, despite the fact that these enzymes are key components for regulating neuromodulation/neurotransmission. Here, an eyestalk ganglia-specific transcriptome was mined for transcripts encoding enzymes involved in neuropeptide, amine, diffusible gas and small molecule transmitter biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Homarus homologs of peptide precursor processing (signal peptide peptidase, prohormone processing protease and carboxypeptidase) and immature peptide modifying (glutaminyl cyclase, tyrosylprotein sulfotransferase, protein disulfide isomerase, peptidylglycine-α-hydroxylating monooxygenase and peptidyl-α-hydroxyglycine-α-amidating lyase) enzymes were identified in the eyestalk assembly. Similarly, transcripts encoding full complements of the enzymes responsible for dopamine [tryptophan-phenylalanine hydroxylase (TPH), tyrosine hydroxylase and DOPA decarboxylase (DDC)], octopamine (TPH, tyrosine decarboxylase and tyramine β-hydroxylase), serotonin (TPH or tryptophan hydroxylase and DDC) and histamine (histidine decarboxylase) biosynthesis were identified from the eyestalk ganglia, as were those responsible for the generation of the gases nitric oxide (nitric oxide synthase) and carbon monoxide (heme oxygenase), and the small molecule transmitters acetylcholine (choline acetyltransferase), glutamate (glutaminase) and GABA (glutamic acid decarboxylase). The presence and identity of the transcriptome-derived transcripts were confirmed using RT-PCR. The data presented here provide a foundation for future gene-based studies of neuromodulatory control at the level of neurotransmitter/modulator biosynthesis in Homarus.