Analysis, characterisation and expression of gill-expressed carbonic anhydrase genes in the freshwater crayfish Cherax quadricarinatus

Effect of abamectin on osmoregulation in red swamp crayfish (Procambarus clarkii)

As a widely used pesticide, abamectin could be a threat to nontarget organisms. In this study, the toxic mechanism of abamectin on osmoregulation in Procambarus clarkii was explored for the first time. The results of this study showed that with increasing abamectin concentration, the membrane structures of gill filaments were damaged, with changes in ATPase activities, transporter contents, biogenic amine contents, and gene expression levels. The results of this study indicated that at 0.2 mg/L abamectin, ion diffusion could maintain osmoregulation. At 0.4 mg/L abamectin, passive transport was inhibited due to damage to the membrane structures of gill filaments, and active transport needed to be enhanced for osmoregulation. At 0.6 mg/L abamectin, the membrane structures of gill filaments were seriously damaged, and the expression level of osmoregulation-related genes decreased, but the organisms were still mobilizing various transporters, ATPases, and biogenic amines to address abamectin stress. This study provided a theoretical basis for further study of the effects of contaminations in aquatic environment on the health of crustaceans.

Identifying low salinity adaptation gene expression in the anterior and posterior gills of the mud crab (Scylla paramamosain) by transcriptomic analysis

In the present study, BGISEQ-500 RNA-Seq technology was adopted to investigate how Scylla paramamosain adapts to salinity tolerance at the molecular level and explores changes in gene expression linked to salinity adaptation following exposure to both low salinity (5 ‰) and standard salinity (23 ‰) conditions. A total of 1100 and 520 differentially expressed genes (DEGs) were identified in the anterior and posterior gills, respectively, and their corresponding expression patterns were visualized in volcano plots and a heatmap. Further analysis highlighted significant enrichment of well-established gene functional categories and signaling pathways, including those what associated with cellular stress response, ion transport, energy metabolism, amino acid metabolism, H2O transport, and physiological stress compensation. We also selected key DEGs within the anterior and posterior gills that encode pivotal stress adaptation and tolerance modulators, including AQP, ABCA1, HSP 10, A35, CAg, NKA, VPA, CAc, and SPS. Interestingly, A35 in the gills might regulate osmolality by binding CHH in response to low salinity stress or serve as a mechanism for energy compensation. Taken together, our findings elucidated the intricate molecular mechanism employed by S. paramamosain for salinity adaptation, which involved distinct gene expression patterns in the anterior and posterior gills. These findings provide the foothold for subsequent investigations into salinity-responsive candidate genes and contribute to a deeper understanding of S. paramamosain's adaptation mechanisms in low-salinity surroundings, which is crucial for the development of low-salinity species cultivation and the establishment of a robust culture model.

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.

Histological, Physiological and Transcriptomic Analysis Reveal the Acute Alkalinity Stress of the Gill and Hepatopancreas of Litopenaeus vannamei

The pacific white shrimp (Litopenaeus vannamei) has gradually become a promising economic species in the development of saline-alkali water fishery. The study related to the stress reaction of pacific white shrimp under alkalinity stress is still limited, which is also a critical limiting factor for its saline-alkaline aquaculture. In this study, we aim to analyse the stress reaction of pacific white shrimp under acute alkalinity stress between control group (alkalinity:40 mg/L) and treatment group (alkalinity:350 mg/L) through histological observation, physiological determination and transcriptome. In the present study, during the process of acute alkalinity stress, the activities of Na+-K+-ATPase, carbonic anhydrase, sodium/hydrogen exchanger in gill related to homeostasis were significantly changed, the activities of superoxide dismutase and catalase related to antioxidant were decreased in both gill and hepatopancreas, and the activities of protease, lipase and amylase in hepatopancreas were decreased. At the same time, different degrees of histological damages were occured in the gill and hepatopancreas under acute alkalinity stress. There were 194 and 236 different expressed genes identified in gill and hepatopancreas respectively. Functional enrichment assessment indicated that the alkalinity stress-related genes in both gill and hepatopancreas were primarily involved in fatty acid metabolism, glycolysis/gluconeogenesis, glycerophospholipid metabolism. The results indicated that the functions of homeostasis regulation, antioxidation and digestion of pacific white shrimp were decreased under acute alkalinity stress, at the same time, the energy metabolism in gill and hepatopancreas were modified to cope with alkalinity stress. This work provides important clues for understanding the response mechanism of pacific white shrimp under acute alkalinity stress.

Effect of high alkalinity on shrimp gills: Histopathological alternations and cell specific responses

High alkalinity stress was considered as a major risk factor for aquatic animals surviving in saline-alkaline water. However, few information exists on the effects of alkalinity stress in crustacean species. As the dominant role of gills in osmotic and ionic regulation, the present study firstly evaluated the effect of alkalinity stress in Exopalaemon carinicauda to determine changes in gill microstructure, and then explore the heterogeneity response of gill cells in alkalinity adaptation by single-cell RNA sequencing (scRNA-seq). Hemolymph osmolality and pH were increased remarkably, and gills showed pillar cells with more symmetrical arrangement and longer lateral flanges and nephrocytes with larger vacuoles in high alkalinity. ScRNA-seq results showed that alkalinity stress reduced the proportion of pillar cells and increased the proportion of nephrocytes significantly. The differentially expressed genes (DEGs) related to ion transport, especially acid-base regulation, such as V(H⁺)-ATPases and carbonic anhydrases, were down-regulated in pillar cells and up-regulated in nephrocytes. Furthermore, pseudotime analysis showed that some nephrocytes transformed to perform ion transport function in alkalinity adaption. Notedly, the positive signals of carbonic anhydrase were obviously observed in the nephrocytes after alkalinity stress. These results indicated that the alkalinity stress inhibited the ion transport function of pillar cells, but induced the active role of nephrocytes in alkalinity adaptation. Collectively, our results provided the new insight into the cellular and molecular mechanism behind the adverse effects of saline-alkaline water and the saline-alkaline adaption mechanism in crustaceans.

Effects of low salinity stress on osmoregulation and gill transcriptome in different populations of mud crab Scylla paramamosain

Animals living in estuaries suffer from rapid and continuous salinity fluctuations, while the global warming and extreme precipitation aggravate this situation. Osmoregulation is important for estuarine animals adapt to salinity fluctuations. The present study investigated the effects of low salinity stress on osmoregulation and gill transcriptome in two populations of mud crab from Hangzhou Bay and Zhangzhou Bay of China, respectively. Crabs were transferred from salinity 25 ppt to 5 ppt for 96 h. Edematous swelling in gill filaments was caused by low salinity stress and was more serious in Zhangzhou Bay population. Gill Na⁺/K⁺-ATPase activity increased (p < 0.01) in both populations under the low salinity stress and was significantly higher (p < 0.01) in Hangzhou Bay population than in Zhangzhou Bay population. According to transcriptome analysis, there were 191 genes differentially expressed under the low salinity stress in gill tissue of both populations. Several ion transport and energy metabolism related pathways, as well as the arginine and proline metabolism pathway, were enriched by these genes. On the other hand, 272 genes were identified to differentially express between two populations under the low salinity stress, but not under the control salinity. The enrichment analysis showed that these genes were mainly related to ion transport, energy metabolism, osmolytes metabolism and methyltransferase activity. In conclusion, the present study suggested that mud crab exploited a combination of extracellular anisosmotic regulation and intracellular isosmotic regulation for osmoregulation under the low salinity stress. Hangzhou Bay population showed a greater osmoregulatory capacity, which is probably due to the enhanced ion transport, energy supply, and osmolytes regulation. Meanwhile, epigenetic modification might also contribute to an inherent osmoregulation ability for Hangzhou Bay population to response to salinity fluctuation rapidly.

Transcriptomic Changes Following Induced De-Masculinisation of Australian Red Claw Crayfish Cherax quadricarinatus

The Australian red claw crayfish Cherax quadricarinatus, an emerging species within the freshwater aquaculture trade, is not only an ideal species for commercial production due to its high fecundity, fast growth, and physiological robustness but also notoriously invasive. Investigating the reproductive axis of this species has been of great interest to farmers, geneticists, and conservationists alike for many decades; however, aside from the characterisation of the key masculinising insulin-like androgenic gland hormone (IAG) produced by the male-specific androgenic gland (AG), little remains known about this system and the downstream signalling cascade involved. This investigation used RNA interference to silence IAG in adult intersex C. quadricarinatus (Cq-IAG), known to be functionally male but genotypically female, successfully inducing sexual redifferentiation in all individuals. To investigate the downstream effects of Cq-IAG knockdown, a comprehensive transcriptomic library was constructed, comprised of three tissues within the male reproductive axis. Several factors known to be involved in the IAG signal transduction pathway, including a receptor, binding factor, and additional insulin-like peptide, were found to not be differentially expressed in response to Cq-IAG silencing, suggesting that the phenotypic changes observed may have occurred through post-transcriptional modifications. Many downstream factors displayed differential expression on a transcriptomic level, most notably related to stress, cell repair, apoptosis, and cell proliferation. These results suggest that IAG is required for sperm maturation, with necrosis of arrested tissue occurring in its absence. These results and the construction of a transcriptomic library for this species will inform future research involving reproductive pathways as well as biotechnological developments in this commercially and ecologically significant species.

Highly sensitive and specific responses of shrimp gill cells to high pH stress based on single cell RNA-seq analysis

High pH is one of the main stressors affecting the shrimp survival, growth, and physiology in aquaculture ponds, but the cellular and molecular mechanism responsible for high pH stress has not been elucidated in shrimp. In this study, the shrimp acid-base disturbance and gill cell alterations were significantly observed and then single cell RNA-sequencing (scRNA-seq) was performed to study the sensitive and specific responses of gill cells to high pH stress. Three main gill cell types, including pillar cells, hemocytes and septal cells were identified. By comparative scRNA-seq analysis between control and pH group, the pillar cell was regarded as the target cell type in response to high pH stress with the down-regulation of ammonia excretion and H+ transport related genes and up-regulation of immune related genes. Notedly, high pH resulted in the emergence of a new immune cell subcluster in pillar cells, with immune activation and stress defense states. Pseudotime analysis also showed that the pillar cells could transform into the functionally inhibited ion cell subclusters and functionally activated immune cell subclusters after high pH stress. Further, the regulatory network of pillar cell population was predicted by WGCNA and two transcription factors were identified. In conclusion, these results provide key insights into the shrimp gill cell-type-specific mechanisms underlying high pH stress response at a single-cell resolution.

Molecular Characterization of Carbonic Anhydrase II (CA II) and Its Potential Involvement in Regulating Shell Formation in the Pacific Abalone, Haliotis discus hannai

Carbonic anhydrases (CAs) are a family of metalloenzymes that can catalyze the reversible interconversion of CO₂/HCO₃^–, ubiquitously present in both prokaryotes and eukaryotes. In the present study, a CA II (designated as HdhCA II) was sequenced and characterized from the mantle tissue of the Pacific abalone. The complete sequence of HdhCA II was 1,169 bp, encoding a polypeptide of 349 amino acids with a NH₂-terminal signal peptide and a CA architectural domain. The predicted protein shared 98.57% and 68.59% sequence identities with CA II of Haliotis gigantea and Haliotis tuberculata, respectively. Two putative N-linked glycosylation motifs and two cysteine residues could potentially form intramolecular disulfide bond present in HdhCA II. The phylogenetic analysis indicated that HdhCA II was placed in a gastropod clade and robustly clustered with CA II of H. gigantea and H. tuberculata. The highest level of HdhCA II mRNA expression was detected in the shell forming mantle tissue. During ontogenesis, the mRNA of HdhCA II was detected in all stages, with larval shell formation stage showing the highest expression level. The in situ hybridization results detected the HdhCA II mRNA expression in the epithelial cells of the dorsal mantle pallial, an area known to express genes involved in the formation of a nacreous layer in the shell. This is the first report of HdhCA II in the Pacific abalone, and the results of this study indicate that this gene might play a role in the shell formation of abalone.

Comparative transcriptome analysis of the gills of Cardisoma armatum provides novel insights into the terrestrial adaptive related mechanism of air exposure stress

Cardisoma armatum is a typical member of the Gecarcinidae which show significant behavioral, morphological, physiological, and/or biochemical adaptations permitting extended activities on the land. The special gills (branchiostegal lung) of C. armatum play an important role in maintaining osmotic pressure balance and obtaining oxygen to adapt to the terrestrial environment. However, adaptive molecular mechanisms responding to air exposure in C. armatum are still poorly understood. In this study, transcriptomic analysis and histological analysis were conducted on the gills to test adaptive capabilities over 8 h between the aerial exposure (AE) and the water immersion (WI) group. Differentially expressed genes (DEGs) related to terrestrial adaptation were categorized into four broad categories: ion transport, acid-base balance, energy metabolism and immune response. This is the first research to reveal the molecular mechanism of terrestrial adaptation in C. armatum, and will provide new insight into the molecular genetic basis of terrestrial adaptation in crabs.

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.

Characterization, functional analysis, and expression levels of three carbonic anhydrases in response to pH and saline-alkaline stresses in the ridgetail white prawn Exopalaemon carinicauda

Carbonate alkalinity, salinity, and pH are three important stress factors for aquatic animals in saline-alkaline water. Carbonic anhydrases (CAs) catalyze the reversible reaction of CO2 reported to play an important role in the acid-base regulation in vertebrates. To explore the molecular mechanism of CAs efficacy in shrimp after their transfer into saline-alkaline water, the cDNAs of three CAs (EcCAc, EcCAg, and EcCAb) were cloned from Exopalaemon carinicauda. Sequence analysis showed that EcCAc and EcCAg both possessed a conserved α-CA domain and a proton acceptor site, and EcCAb contained a Pro-CA domain. Tissue expression analysis demonstrated that EcCAc and EcCAg were most abundantly in gills, and EcCAb was highly expressed in muscle. The cumulative mortalities remained below 25% under exposure to pH (pH 6 and pH 9), low salinity (5 ppt), or high carbonate alkalinity (5 and 10 mmol/L) after 72 h of exposure. However, mortalities increased up to 70% under extreme saline-alkaline stress (salinity 5 ppt, carbonate alkalinity 10 mmol/L, and pH 9) after 14 days of exposure. The EcCAc and EcCAg expressions in gills were significantly upregulated during the early period of pH and saline-alkaline stresses, while the EcCAb expressions showed no regular or large changes. The two-way ANOVA found significant interactions between salinity and carbonate alkalinity observed in EcCAc, EcCAg, and EcCAb expressions (p < 0.05). Furthermore, an RNA interference experiment resulted in increased mortality of EcCAc- and EcCAg-silenced prawns under saline-alkaline stress. EcCAc knockdown reduced expressions of Na+/H+ exchanger (EcNHE) and sodium bicarbonate cotransporter (EcNBC), and EcCAg knockdown reduced EcCAc, EcNHE, EcNBC, and V-type H+-ATPase (EcVTP) expressions. These results suggest EcCAc and EcCAg as important modulators in response to pH and saline-alkaline stresses in E. carinicauda.

Involvement of β-Carbonic Anhydrase Genes in Bacterial Genomic Islands and Their Horizontal Transfer to Protists

Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes that produce proteins that contribute to a variety of functions, including, but not limited to, the regulation of cell metabolism, antimicrobial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside reproduction, is called horizontal gene transfer (HGT). Previous data have shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes. β-Carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We previously suggested the horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have been transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists.IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs is exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as environment- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical biochemical pathways, such as the regulation of pH homeostasis and electrolyte transfer. Among the six evolutionary families of CAs, β-CA gene sequences are present in many bacterial species, which can be horizontally transferred to protists during evolution. This study shows the involvement of bacterial β-CA gene sequences in the GIs and suggests their horizontal transfer to protists during evolution.

Adaptation of the white shrimp Litopenaeus vannamei to gradual changes to a low-pH environment

pH variation could cause a stress response in euryhaline penaeids, we evaluated the mortality, growth performance, osmoregulation gene expression, digestive enzyme activity, histology, and resistance against Vibrio parahemolyticus of white shrimp Litopenaeus vannamei reared under conditions of gradual changes to a low-pH environment (gradual-low pH, 6.65-8.20) or a high-pH environment (gradual-high pH, 8.20-9.81) versus a normal pH environment (8.14-8.31) during a 28-d experiment. Consequently, under gradual-high pH, the cumulative mortality rate (CMR) rose with time until 39.9% on days 28; the weight gain percentage (WGP) and length gain percentage (LGP) decreased continuously. However, under gradual-low pH, the CMR of shrimp stabilized at 6.67% during 7-28 d; the WGP and LGP decreased first and then returned to normal. These results indicated that L. vannamei displayed a moderate tolerance to gradual-low pH, compared with gradual-high pH. Under gradual-low pH, the Na⁺/K⁺-ATPase, cytoplasmic carbonic anydrase (CAc), and glycosyl-phosphatidylinositol-linked carbonic anhydrase (CAg) transcripts of shrimp increased continuously or then back to normal; the amylase, lipase, and trypsin activities decreased first and then returned to normal or increased; the hepatopancreases and midguts showed histopathological lesions first and then got remission. Thus, the major adaptation mechanism of shrimp to gradual-low pH might be its high osmoregulation ability, which made shrimp achieve a new, balanced steady-state, then promoted longer intestinal villi and recuperative hepatopancreases of shrimp with enhanced digestive enzyme activities to increase nutrient absorption after long-term exposure. Meanwhile, the enhanced resistance against V. parahemolyticus under gradual-low pH would probably inhibit disease outbreak in the shrimp farming.

Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii

Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA), Na⁺/K⁺-ATPase (NKA), H⁺-ATPase (HAT), Na⁺/K⁺/2Cl⁻ cotransporter (NKCC), Na⁺/Cl⁻/HCO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{3}^{-}$\end{document}3− cotransporter (NBC), Na⁺/H⁺ exchanger (NHE), Arginine kinase (AK), Sarcoplasmic Ca⁺²-ATPase (SERCA) and Calreticulin (CRT). We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish, Cherax quadricarinatus, C. destructor and C. cainii, with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the three Cherax sp. Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84%) and gills (78%) and the lowest in testes (66%). The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE) were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of other basic physiological functions in different tissue types.

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)

Background

The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater.

Methods

The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597.

Results

In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation.

Discussion

The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobrachium prawns and other crustaceans more broadly.

Expression patterns of two carbonic anhydrase genes, Na+/K+-ATPase and V-type H+-ATPase, in the freshwater crayfish, Cherax quadricarinatus, exposed to low pH and high pH

Carbonic anhydrase (CA), Na+/K+-ATPase (NKA) and Vacuolar-type H+-ATPase (HAT) play vital roles in osmoregulation and pH balance in decapod crustaceans. As variable pH levels have a significant impact on the physiology of crustaceans, it is crucial to understand the mechanisms by which an animal maintains its internal pH. We examined expression patterns of cytoplasmic (CAc) and membrane-associated form (CAg) of CA, NKA α subunit and HAT subunit a in gills of freshwater crayfish, Cherax quadricarinatus, at three pH levels – 6.2, 7.2 (control) and 8.2 – over 24 h. Expression levels of CAc were significantly increased at low pH and decreased at high pH conditions 24 h after transfer. Expression increased at low pH after 12 h, and reached its maximum level by 24 h. CAg showed a significant increase in expression at 6 h after transfer at low pH. Expression of NKA significantly increased at 6 h after transfer to pH 6.2 and remained elevated for up to 24 h. Expression for HAT and NKA showed similar patterns, where expression significantly increased 6 h after transfer to low pH and remained significantly elevated throughout the experiment. Overall, CAc, CAg, NKA and HAT gene expression is induced at low pH conditions in freshwater crayfish.

Transcriptomic characterization and curation of candidate neuropeptides regulating reproduction in the eyestalk ganglia of the Australian crayfish, Cherax quadricarinatus

The Australian redclaw crayfish (Cherax quadricarinatus) has recently received attention as an emerging candidate for sustainable aquaculture production in Australia and worldwide. More importantly, C. quadricarinatus serves as a good model organism for the commercially important group of decapod crustaceans as it is distributed worldwide, easy to maintain in the laboratory and its reproductive cycle has been well documented. In order to better understand the key reproduction and development regulating mechanisms in decapod crustaceans, the molecular toolkit available for model organisms such as C. quadricarinatus must be expanded. However, there has been no study undertaken to establish the C. quadricarinatus neuropeptidome. Here we report a comprehensive study of the neuropeptide genes expressed in the eyestalk in the Australian crayfish C. quadricarinatus. We characterised 53 putative neuropeptide-encoding transcripts based on key features of neuropeptides as characterised in other species. Of those, 14 neuropeptides implicated in reproduction regulation were chosen for assessment of their tissue distribution using RT-PCR. Further insights are discussed in relation to current knowledge of neuropeptides in other species and potential follow up studies. Overall, the resulting data lays the foundation for future gene-based neuroendocrinology studies in C. quadricarinatus.

In vivo effects of Aphanizomenon flos-aquae DC-1 aphantoxins on gas exchange and ion equilibrium in the zebrafish gill

Aphantoxins, neurotoxins or paralytic shellfish poisons (PSPs) generated by Aphanizomenon flos-aquae, are a threat to environmental safety and human health in eutrophic waters worldwide. The molecular mechanisms of neurotoxin function have been studied; however, the effects of these neurotoxins on oxidative stress, ion transport, gas exchange, and branchial ultrastructure in fish gills are not fully understood. Aphantoxins extracted from A. flos-aquae DC-1 were detected by high-performance liquid chromatography. The major ingredients were gonyautoxins 1 and 5 and neosaxitoxin, which comprised 34.04%, 21.28%, and 12.77% of the total, respectively. Zebrafish (Danio rerio) were administered A. flos-aquae DC-1 aphantoxins at 5.3 or 7.61μg saxitoxin equivalents (eq)/kg (low and high doses, respectively) by intraperitoneal injection. The activities of Na(+)-K(+)-ATPase (NKA), carbonic anhydrase (CA), and lactate dehydrogenase (LDH), ultrastructural alterations in chloride and epithelial cells, and reactive oxygen species (ROS) and total antioxidative capacity (T-AOC) were investigated in the gills during the first 24h after exposure. Aphantoxins significantly increased the level of ROS and decreased the T-AOC in zebrafish gills from 3 to 12h post-exposure, suggesting an induction of oxidative stress and inhibition of antioxidant capacity. Reduced activities of NKA and CA demonstrated abnormal ion transport and gas exchange in the gills of aphantoxin-treated fish. Toxin administration also resulted in increased LDH activity and ultrastructural alterations in chloride and epithelial cells, suggesting a disruption of function and structure in zebrafish gills. The observed abnormalities in zebrafish gills occurred in a time- and dose-dependent manner. These findings demonstrate that aphantoxins or PSPs may inhibit ion transport and gas exchange, increase LDH activity, and result in ultrastructural damage to the gills through elevations in oxidative stress and reduced antioxidant capacity. These effects of aphantoxins in the gills of zebrafish suggest an induction of respiratory toxicity. The parameters investigated in this study may be also considered as biomarkers for studying aphantoxin/PSP exposure and cyanobacterial blooms in nature.

Metabolic product response profiles of Cherax quadricarinatus towards white spot syndrome virus infection

White spot syndrome virus (WSSV) is one of the most devastating viral pathogens in both shrimp and crayfish farms, which often causes disease outbreak and leads to massive moralities with significant economic losses of aquaculture. However, limited research has been carried out on the intrinsic mechanisms toward WSSV challenge at the metabolic level. To gain comprehensive insight into metabolic responses induced by WSSV, we applied an NMR approach to investigate metabolic changes of crayfish gill and hepatopancreas infected by WSSV for 1, 6 and 12 h. In gill, an enhanced energy metabolism was observed in WSSV-challenged crayfish samples at 1 h, as marked by increased glucose, alanine, methionine, glutamate and uracil. Afterwards, energy metabolism, lipid metabolism as well as osmoregulation were markedly increased at 6 hpi, as shown by elevated glucose, alanine, methionine, fumarate, tyrosine, tryptophan, histidine, phosphorylcholine, betaine and uracil, whereas no obvious metabolites change was detected at 12 hpi. As for hepatopancreas, disturbed lipid metabolism and induced osmotic regulation was found at 6 hpi based on the metabolic biomarkers such as branched chain amino acids, threonine, alanine, methionine, glutamate, glutamine, tyrosine, phenylalanine, lactate and lipid. However, no obvious metabolic change was shown in hepatopancreas at both 1 hpi and 12 hpi. Taken together, our present results provided essential metabolic information about host-pathogen interactions in crayfish, which shed new light on our understanding of WSSV infection at metabolic level.

Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis

Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype-phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.

Transcriptome analysis and characterisation of gill-expressed carbonic anhydrase and other key osmoregulatory genes in freshwater crayfish Cherax quadricarinatus

The pH and salinity balance mechanisms of crayfish are controlled by a set of transport-related genes. We identified a set of the genes from the gill transcriptome from a freshwater crayfish Cherax quadricarinatus using the Illumina NGS-sequencing technology. We identified and characterized carbonic anhydrase (CA) genes and some other key genes involved in systematic acid-base balance and osmotic/ionic regulation. We also examined expression patterns of some of these genes across different sublethal pH levels [1]. A total of 72,382,710 paired-end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. About 37% of the contigs received significant BLAST hits and 22% were assigned gene ontology terms. These data will assist in further physiological-genomic studies in crayfish.