High salinity induced expression profiling of differentially expressed genes in shrimp (Penaeus monodon)

Transcriptomic analysis of Penaeus monodon in response to acute and chronic hypotonic stress

To investigate the different mechanisms of Penaeus monodon in response to acute and chronic hypotonic stress, RNA sequencing technology was employed to profile the gene expression patterns in the gill, hepatopancreas, and hemocyte at 0, 6, 48, and 72 h post acute hypotonic stress treatment (with salinity immediately decreased from 20 psu to 4 psu) and at 0, 2, 10, 15 days during chronic hypotonic stress treatment (with salinity gradually decreased from 20 psu to 4 psu). The control group (SC) was maintained at a constant salinity of 20 psu. Differentially expressed genes (DEGs) were identified, followed by further validation using real-time quantitative reverse transcription PCR (RT-qPCR). A total of 34,217 genes were expressed through sequencing. Compared with the control group, 8,503 DEGs were identified in the acute hypotonic stress group, comprising 3,266 up-regulated and 5,237 down-regulated genes. In the chronic hypotonic stress group, 8,900 DEGs were detected, including 3,019 up-regulated and 5,881 down-regulated genes. Gene Ontology (GO) functional annotation analysis indicated that DEGs were primarily enriched in biological processes such as cellular and metabolic processes, cellular components like membrane and other cellular components, and molecular functions including structural binding and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that DEGs were predominantly concentrated in five major pathways: metabolism, genetic information processing, environmental information processing, cellular processes, and biological systems. These pathways encompassed antigen processing and presentation, the NOD-like receptor signaling pathway, the Toll-like receptor signaling and cell apoptosis. The RT-qPCR validation of 11 DEGs (hsp70, hsp90, nlrp3, mincle, nlrp12, tlr4, myd88, imd, casp7, casp9 and toll) demonstrated that the trends observed in the quantitative results were consistent with those from the transcriptome analysis, thereby validating the reliability of transcriptome sequencing data. This study identified that hypotonic stress triggers physiological responses in P. monodon to both acute and chronic hypotonic conditions, offering valuable insights into the expression patterns of functional genes in the gills, hepatopancreas, and hemocytes of P. monodon under such stress. These findings provide foundational data and a theoretical basis for further research into the regulatory mechanism of P. monodon in response to hypotonic stress.

Transcriptomic variations associated with salinity stress in Penaeus indicus

BACKGROUND

The Indian white shrimp, Penaeus indicus a native species of India, is important brackishwater aquaculture species. Shrimps are euryhaline in nature and they regulate osmotic and ionic concentrations by osmoregulatory process. However, variations in abiotic factors such as salinity result in stress to the shrimps during culture period affecting their growth and immunity.

METHODS AND RESULTS

To understand the adaptive mechanism to stress in low salinity conditions, RNA-seq was used to compare the transcriptomic response of P. indicus upto 3 weeks. De novo assembly using Trinity assembler generated a total of 173,582 transcripts. The assembly had a mean length of 854 bp, N50 value of 1243 bp and GC content of 42.33%. Differential gene expression analysis, resulted in identification of 2130, 3090, and 5351 DEGs in 7 days, 14 days and 21 days respectively of salinity stress period. The pathway prediction of the assembled trinity transcripts using KEGG database showed total number of 329 pathways linking 12,430 transcripts. KEGG pathway enrichment analyses led to the identification of several enriched pathways related to lipid metabolism, amino acid metabolism, glycolysis, signalling pathways etc. Selected genes involved in osmoregulatory process and immune response in shrimps were validated and analysed for the gene expression levels by quantitative real-time PCR (qPCR).

CONCLUSION

This study on the adaptive transcriptomic response of P. indicus to low salinity, will further help in our understanding of the molecular mechanisms underlying osmoregulation mechanism in shrimps.

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.

Identification of key immune and stress related genes and pathways by comparative analysis of the gene expression profile under multiple environmental stressors in pacific white shrimp (Litopenaeus vannamei)

Water salinity, pH, and nitrite concentration are considered environmental factors affecting the growth rate, survival, health, and physiological conditions of aquatic animals. The identification of key genes that are involved in the response to environmental stressors is essential for controlling stress in aquatic animals and sustainable aquaculture. In this study, RNA sequencing was performed to identify the differentially expressed genes (DEGs) and biological pathways that are involved in the response of the hepatopancreas to environmental stressors, including low salinity stress, nitrite stress, low pH stress, and high pH stress. The DEGs were enriched in biological pathways related to immune response, energy metabolism, oxidative stress response, hemostasis, and enzymatic activity of the hepatopancreas. In addition to the identification of DEGs related to each stressor, some DEGs were found to be expressed among all groups. The most important overlapping DEGs under multiple stressors were juvenile hormone esterase-like protein 2 (JHE-like), myosin light chain, C-type lectin 2, myosin-9-like, anti-lipopolysaccharide factor 1 (ALF-1), peroxisomal acyl-coenzyme An oxidase 1-like (ACX1), hepatic lectin-like, venom phosphodiesterase 2-like, hemolymph clottable protein-like (CP), cathepsin L, and Ras-like protein 2. The results of the present study provide additional information regarding the transcriptional response of the hepatopancreas to low salinity, nitrite, low pH, and high pH stress. Moreover, the discovery of several overlapping DEGs among different stressors provided a better understanding of the molecular function of the hepatopancreas.

Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp Marsupenaeus japonicus acclimated at different salinities

Shrimps inhabiting the coastal water can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after acclimating for 24 h. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. In particular, the increase of the expression level of the gene encoding glutamate-ammonia ligase which functions in the glutamine metabolism appeared to be relevant to the increased glutamine concentration at high salinity. Furthermore, the alanine concentration increased at high salinity was likely to be associated with the decrease in the expression levels of the alanine-glyoxylate transaminase gene. Thus, there is a possibility that changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are regulated by changes in the expression levels of genes related to amino acid metabolism.

Molecular characterization and organ-specific expression of the gene that encodes betaine aldehyde dehydrogenase from the white shrimp Litopenaeus vannamei in response to osmotic stress

Crustaceans overcome osmotic disturbances by regulating their intracellular concentration of ions and osmolytes. Glycine betaine (GB), an osmolyte accumulated in response to hyperosmotic stress, is synthesized by betaine aldehyde dehydrogenase (BADH EC 1.2.1.8) through the oxidation of betaine aldehyde. A partial BADH cDNA sequence from the white shrimp Litopenaeus vannamei was obtained and its organ-specific expression during osmotic stress (low and high salinity) was evaluated. The partial BADH cDNA sequence (LvBADH) is 1103bp long and encodes an open reading frame for 217 protein residues. The amino acid sequence of LvBADH is related to that of other BADHs, TMABA-DH and ALDH9 from invertebrate and vertebrate homologues, and includes the essential domains of their function and regulation. LvBADH activity and mRNA expression were detected in the gills, hepatopancreas and muscle with the highest levels in the hepatopancreas. LvBADH mRNA expression increased 2-3-fold in the hepatopancreas and gills after 7days of osmotic variation (25 and 40ppt). In contrast, LvBADH mRNA expression in muscle decreased 4-fold and 15-fold after 7days at low and high salinity, respectively. The results indicate that LvBADH is ubiquitously expressed, but its levels are organ-specific and regulated by osmotic stress, and that LvBADH is involved in the cellular response of crustaceans to variations in environmental salinity.