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

Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo

Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.

Metabolomic responses based on transcriptome of the hepatopancreas in Exopalaemon carinicauda under carbonate alkalinity stress

High carbonate alkalinity is one of the major stress factors for survival of aquatic animals in saline-alkaline water. Exopalaemon carinicauda is a good model for studying the saline-alkaline adaption mechanism in crustacean because of its great adaptive capacity to alkalinity stress. In this study, non-targeted liquid chromatography-mass spectrometry (LC-MS) metabolomics analyses based on high-throughput RNA sequencing (RNA-Seq) were used to study the metabolomic responses of hepatopancreas in E. carinicauda at 12 h and 36 h after acute carbonate alkalinity stress. The results revealed that most of the significantly differential metabolites were related to the lipid metabolism. In particular, the sphingolipid metabolism was observed at 12 h, the glycerophospholipid metabolism was detected at 36 h, and the linoleic acid metabolic pathway was significantly enriched at both 12 h and 36 h. The combined transcriptome and metabolome analysis showed that energy consumption increased at 12 h, resulting in significant enrichment of AMPK signaling pathways, which contributed to maintain energy homeostasis. Subsequently, the hepatopancreas provided sufficient energy supply through cAMP signaling pathway and glycerophosphate metabolism to maintain normal metabolic function at 36 h. These findings might help to understand the molecular mechanisms of the E. carinicauda under carbonate alkalinity stress, thereby promote the research and development of saline-alkaline resistant shrimp.

Rapid adaptive and acute stimulatory responses to low salinity stress in Pacific white shrimp (Litopenaeus vannamei): Insights from integrative transcriptomic and proteomic analysis

The Pacific white shrimp (Litopenaeus vannamei) is a euryhaline crustacean capable of tolerating a wide range of ambient salinity, but the strategies of hepatopancreas to rapid adaptive or acute stimulatory responses to extremely low salinity fluctuations remains unclear. In this study, we integrated transcriptomic and proteomic analyses on the hepatopancreas derived from rapid adaptative (RA) and acute stimulatory (AS) responses to extremely low salinity stress (0.3 ppt) to unveil specific regulatory mechanisms. The RA group displayed normal epithelial cells and tubule structures, while the AS group showed histological changes and lesions. A total of 754 and 649 differentially expressed genes (DEGs) were identified in RA and AS treatments, respectively. For proteome, a total of 206 and 66 differentially expressed proteins (DEPs) were obtained in the RA/CT and AS/CT comparison groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted among the DEGs and DEPs, revealing that metabolic related pathways were significantly enriched pathways in both comparison groups. In addition, correlation analysis of transcriptomic and proteomic results showed that 20 and 3 pairs of DEGs/DEPs were identified in RA vs. CT and AS vs. CT comparison groups, respectively. This study is the first report on the rapid adaptive and acute stimulatory transcriptomic and proteomic responses of L. vannamei to extremely low salinity, shedding light on the mechanisms underlying osmoregulation in euryhaline crustaceans.

Cloning, identification, and functional characterization of novel prophenoloxidases (ShproPO) from the freshwater crab Sinopotamon henanense in response to cadmium exposure and Aeromonas hydrophila infection

Prophenoloxidase (proPO) is essential in the prophenoloxidase-activating system (proPO-AS) which is important for defense against foreign infection in crustaceans. However, most studies have focused on expression in the presence of a single pathogenic bacterium, and very few have addressed the presence of environmental contaminants simultaneously, such as cadmium (Cd) and Aeromonas hydrophila. Our study aimed to investigate the function of proPO in the freshwater crab Sinopotamon henanense and the changes in its expression by Cd and infection of A. hydrophila. A novel proPO from the hemocytes of S. henanense (ShproPO) was found in this research, the full-length cDNA of ShproPO was 2620 bp of encoding a protein of 678 amino acids containing three typical hemocyanin domains. The ShproPO protein could be found in both the granular (GHc) and the semi-granular hemocytes (SGHc). The ShproPO mRNA was found to be abundantly expressed in hemocytes and could be influenced by A. hydrophila infection. These results indicate that ShproPO could be involved in the antibacterial process. Further research found that low concentrations of Cd could promote its expression after infection with A. hydrophila. Therefore, it was hypothesized that Cd disrupted the response of crabs to A. hydrophila infection. Subsequently, PO enzyme activity was found to be significantly reduced through in vivo RNA interference with ShproPO, and the results suggested that ShproPO is likely to be a key enzyme in the melanization response. Finally, ShproPO was found to significantly enhance the phagocytosis of A. hydrophila-infected hemocytes by in vitro recombination, confirming that ShproPO is involved in hemocyte-mediated melanization and phagocytosis. Our findings reveal completely new insight into the immunotoxicity of Cd and the immune function of ShproPO in S. henanense.

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.

Effects of Low Temperature on Antioxidant and Heat Shock Protein Expression Profiles and Transcriptomic Responses in Crayfish (Cherax destructor)

Low temperature is a critical factor restricting the growth and survival of aquatic animals, but research on the mechanism of response to low temperature in Cherax destructor is limited. C. destructor is one of the most important freshwater crustaceans with strong adaptability in Australia, and it has been commercialized gradually in recent years. Here, growth indicators, antioxidant parameters, anti-stress gene expression, and transcriptome sequencing were used on crayfish following 8 weeks of low-temperature acclimation. The results showed that weight gain, length gain, and molting rates decreased as the temperature decreased. The activity of antioxidant enzymes decreased, while the content of antioxidant substances and the expression of anti-stress genes increased. Transcriptome sequencing identified 589 differentially expressed genes, 279 of which were upregulated and 310 downregulated. The gene functions and pathways for endocrine disorders, glucose metabolism, antioxidant defense, and immune responses were identified. In conclusion, although low-temperature acclimation inhibited the basal metabolism and immune ability of crayfish, it also increased the antioxidant substance content and anti-stress-gene expression to protect the organism from low-temperature damage. This study provided molecular insights into the study of low-temperature responses of low-temperature-tolerant crustacean species.

Transcriptome analysis of the gills of Eriocheir sinensis provide novel insights into the molecular mechanisms of the pH stress response

Eriocheir sinensis is an important economic species in China, which is easily affected by pH changes. However, the molecular mechanism of the pH stress response in E. sinensis is still unclear. Therefore, this study aimed to examine the molecular response mechanism of E. sinensis based on pH variation surveillance, histopathological evaluation and transcriptomic analyses. Firstly, pH variation surveillance showed that E. sinensis could actively regulate the pH of its environment. Meanwhile, the histopathological evaluation suggested that pH stress seriously damaged the gills, especially at high pH. Finally, transcriptome analysis showed that the expression of genes related to ion transport, immune stress, and energy metabolism significantly changed. Many genes played an important role in the pH response of E. sinensis, such as carbonic anhydrase (CA), mitochondrial proton/calcium exchanger protein (LETM1), recombinant sodium/hydrogen exchanger 3 (SLC9A3/NHE3), heat shock protein 90 alpha family class a member (HSP90A), alkylglycerone phosphate synthase (AGPS), succinate-CoA ligase ADP-forming subunit beta (LSC2), and superoxide dismutase (SOD). Our study revealed the molecular response mechanism of E. sinensis in response to pH stress, thus providing a basis for further research on the molecular mechanism of response to pH stress in aquatic animals.

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.

Growth, biochemical, antioxidants, metabolic enzymes and hemocytes population of the shrimp Litopenaeus vannamei exposed to acidified seawater

Acidification in the marine environment has become a global issue that creates serious threats to marine organisms. In the present study, we evaluated the effect of CO₂ driven acidification on the shrimp Litopenaeus vannamei post-larvae (PL). L. vannamei PL were exposed to six different CO₂ driven acidified seawater, such as 8.2 (control), pH 7.8 (IPCC-predicted ocean pH by 2100), 7.6, 7.4, 7.2 and 7.0 with corresponding pCO₂ level of 380.66, 557.53, 878.55, 1355.48, 2129.46, and 3312.12 μatm for seven weeks. At the end of the acidification experiment, results revealed that the survival, growth, feed index, biochemical constituents, chitin, minerals (Na, K, and Ca), and hemocyte populations of shrimps were found to be significantly decreased in CO₂ driven acidified seawater which indicates the negative impacts of acidified seawater on these parameters in L. vannamei. Further, the level of antioxidants, lipid peroxidation, and metabolic enzymes were significantly higher in the muscle of shrimps exposed to acidified seawater suggests that the L. vannamei under oxidative stress and metabolic stress. Among the various acidified seawater tested, pH 7.6 to 7.0 produced a significantly adverse effect on shrimps. Hence, the present study concluded that the elevated level of seawater acidification can produce harmful effects on the biology and physiology of the commercially important shrimp L. vannamei PL.

Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei)

High-pH tolerance and growth are important traits for the shrimp culture industry in areas with saline-alkali water. In the present study, an F1 full-sib family of Pacific white shrimp (Litopenaeus vannamei) was generated with a new "semidirectional cross" method, and double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology was applied to genotype the 2 parents and 148 progenies. A total of 3567 high-quality markers were constructed for the genetic linkage map, and the total map length was 4161.555 centimorgans (cM), showing 48 linkage groups (LGs) with an average interlocus length of 1.167 cM. With a constrained logarithm of odds (LOD) score ≥ 2.50, 12 high-pH tolerance and 2 growth (body weight) QTLs were located. L. vannamei genomic scaffolds were used to assist with the detection of 21 stress- and 5 growth-related scaffold genes. According to the high-pH transcriptome data of our previous study, 6 candidate high-pH response genes were discovered, and 5 of these 6 genes were consistently expressed with the high-pH transcriptome data, validating the locations of the high-pH tolerance trait-related QTLs in this study. This paper is the first report of fine-mapping high-pH tolerance and growth (body weight) trait QTLs in one L. vannamei genetic map. Our results will further benefit marker-assisted selection work and might be useful for promoting genomic research on the shrimp L. vannamei.

Molecular characterization of a RNA polymerase (RNAP) II (DNA directed) polypeptide H (POLR2H) in Pacific white shrimp (Litopenaeus vannamei) and its role in response to high-pH stress

RNA polymerase (RNAP) II (DNA-directed) (POLR2) genes are essential for cell viability under environmental stress and for the transfer of biological information from DNA to RNA. However, the function and characteristics of POLR2 genes in crustaceans are still unknown. In the present study, a POLR2H cDNA was isolated from Pacific white shrimp (Litopenaeus vannamei) and designated as Lv-POLR2H. The full-length Lv-POLR2H cDNA is 772 bp in length and contains a 32-bp 5'- untranslated region (UTR), a 284-bp 3'- UTR with a poly (A) sequence, and an open reading frame (ORF) of 456 bp encoding an Lv-POLR2H protein of 151 amino acids with a deduced molecular weight of 17.21 kDa. The Lv-POLR2H protein only contains one functional domain, harbors no transmembrane domains and mainly locates in the nucleus. The expression of the Lv-POLR2H mRNA was ubiquitously detected in all selected tissues, with the highest level in the gills. In situ hybridization (ISH) analysis showed that Lv-POLR2H was mainly located in the secondary gill filaments, the transcript levels of Lv-POLR2H in the gills were found to be significantly affected after challenge by pH, low salinity and high concentrations of NO₂^- and NH₄⁺, indicating that Lv-POLR2H in gill tissues might play roles under various physical stresses. Specifically, under high-pH stress, knockdown of Lv-POLR2H via siRNA significantly decreased the survival rate of the shrimp, indicating its key roles in the response to high-pH stress. Our study may provide the first evidence of the role of POLR2H in shrimp responding to high-pH stress and provides new insight into molecular regulation in response to high pH in crustaceans.

Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars

MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into two groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and Baxi banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4 (Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. But they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4.