Search Results (41)

Salinity serves as an important environmental factor in ecosystems, driving the evolution of adaptive strategies in euryhaline species. The Pacific white shrimp, Litopenaeus vannamei, is a representative euryhaline species. However, the molecular mechanisms, particularly the roles of cis-regulatory elements, remain elusive in penaeid shrimp. This study tackles this gap by subjecting L. vannamei to a gradual reduction in salinity from 30‰ to 3‰, and then applying ATAC-seq and RNA-seq techniques to dissect the cis-regulation mechanisms underlying low salinity adaptation. A key finding reveals a positive correlation between chromatin accessibility and gene expression, with 36.8% of differentially expressed genes directly associated with changes in chromatin accessibility. The cis-regulation of many osmoregulation-related pathways, such as betaine synthesis and PI3K-Akt signaling pathways, appeared to be a crucial strategy for salinity adaptation in shrimp. By analyzing differentially accessible regions under low salinity stress, we uncovered two known and seven novel candidate transcription factors (TFs) that may play pivotal roles in salinity adaptation. We further conducted a comprehensive analysis of these TFs, including their functions, expression profiles, consensus TFBS motifs, and the functional enrichment and expression profiles of their targeted genes. This study elucidates a complex cis-regulatory network that enables exceptional salinity tolerance in L. vannamei, which provides a foundation for the refinement of genetic breeding programs and desalination aquaculture for penaeid shrimp. Full article

The habitat characteristics preferred by Penaeus shrimp inhabiting positive (freshwater-dominated) estuaries in North America have been scarcely investigated. Identifying the main environmental factors within the estuary that affect shrimp abundance is relevant to understanding habitat utilization within this particular nursery habitat. This study aimed to evaluate the distribution of penaeid shrimp species along the Soto La Marina River estuary (Northeastern Mexico), analyzing the influence of abiotic factors (water temperature, salinity, and dissolved oxygen) and submerged aquatic vegetation biomass on shrimp populations. A total of 1069 shrimp belonging to four penaeid species (Penaeus aztecus, P. duorarum, P. brasiliensis, and P. setiferus) were collected. Except for P. setiferus, the highest shrimp abundance was near the mouth of the estuary, where the highest salinity and seagrass biomass (Halodule wrightii) were recorded. Salinity and seagrass biomass were the main factors influencing penaeids’ spatial preferences along the estuary, showing significant positive relationships with shrimp abundance in most of the cases examined. Penaeus setiferus was the only species exhibiting peak abundance in an estuarine area devoid of aquatic vegetation (without seagrass or macroalgae) and with a significantly lower salinity level (ca. 22 ppt) than the levels recorded near the river mouth (ca. 28–32 ppt). Differences in osmotic capacity between the species, the protective function of seagrasses against currents, and their role as feeding and refuge habitats could explain the observed spatial distribution in the estuary. Full article

Penaeid shrimp, with its genomes enriched in short tandem repeats (STRs), presents an ideal model for studying the distribution and biological functions of STRs. In this study, we systematically identified and compared STRs across multiple species, confirming a significantly higher prevalence of STRs (26–32%) in penaeid shrimp, which is markedly higher than that observed in other species, such as mammals (1.3–2.1%) and plants (0.21–0.73%). Further analysis utilizing a cohort of 326 Pacific white shrimp revealed a total of 672,507 high-quality STRs evenly distributed across the genome, with a notably lower frequency of SNPs within these STR regions. Focusing on growth traits as a case study, we conducted a genome-wide association study (GWAS) and correlation analyses to identify the regulatory relationship of STRs on complex traits. We discovered 84 STRs that showed a significant association with body weight. Interestingly, eleven of these STRs, with 81% being composed of an A/T base, showed a significant linear correlation with body weight, revealing the key role of A/T-related STRs in shrimp weight regulation. For instance, a significant association and a negative correlation were found between the copy number of the STR [(A)n] at NW_020872788.1:580574 and body weight. The cytokinesis protein 7-like (LOC113800912) gene, which contains this STR in its splice region, exhibits differential expression associated with body weight variation. These findings introduce a model for STR copy number regulation in non-human species, illuminating the influence of STRs on growth traits. It offers a valuable framework for investigating complex traits and the biological functions of STRs in agricultural animals. Full article

Fenneropenaeus merguiensis is one of the largest species of penaeid shrimp. It has a wide distribution of germplasm resources in the South China Sea and the southeastern coastal regions of China, yet its germplasm characteristics remain insufficiently understood. Therefore, we conducted analyses of basic nutritional components, amino acids, fatty acids, antioxidant indices, and genetic diversity in three F. merguiensis populations (FmRP, FmSZ, FmSY). The results showed a significant difference in ash content, with FmSZ having the highest ash content (1.77 g/100 g) (p < 0.05). A total of 17 amino acids were detected, and FmSZ exhibited higher concentrations of most amino acids, especially essential amino acids (p < 0.05). The analysis of fatty acid composition revealed significant differences between the populations, with FmSY potentially having a nutritional advantage overall (p < 0.05). In terms of antioxidant capacity and genetic diversity, there were no significant differences in total antioxidant capacity (T-AOC), catalase (CAT), or superoxide dismutase (SOD) among the populations (p > 0.05). However, genetic analysis indicated that FmSZ had the lowest inbreeding coefficient and relatively higher genetic diversity. In conclusion, among the three F. merguiensis populations, FmSZ has relatively higher nutritional quality and genetic diversity, and F. merguiensis is a high-quality aquatic product worth promoting. The analysis and characterization of various aspects of F. merguiensis from the three locations provide important information and data support for germplasm resources and genetic breeding efforts. Full article

This study assessed catch composition, size selectivity, and fishing efficiency of demersal trawls targeting penaeid shrimp species in the Red Sea. It first compared the currently used diamond mesh codends in two fishing areas, Al Qunfudhah and Jazan, and then compared alternative square mesh codends to diamond mesh codends in Jazan. A total of 33 valid hauls were conducted in 2023, yielding 10,869 kg of total catch. The results showed that the square mesh codend significantly improved size selectivity, particularly for Penaeus semisulcatus and Metapenaeus monoceros, with L₅₀ (50% retention length) values closer to their size at first maturity. The fishing efficiency indicators revealed a reduced retention probability for undersized individuals with square mesh codends. Additionally, bycatch discard rates decreased, indicating potential benefits for ecosystem conservation. This study suggests incorporating square mesh codends into fishery management regulations to enhance size selectivity and reduce bycatch during Red Sea shrimp trawling. Establishing a legal minimum landing size requirement is recommended to complement these efforts and promote sustainable fishing practices. Full article

Biofloc technology (BFT) offers an innovative eco-friendly approach that is particularly applicable in shrimp farming. Penaeus vannamei is the most important seafood species in terms of global economic value. Nevertheless, its increasing global demand highlights the necessity for sustainable production of P. vannamei shrimps outside their native range, assuring the avoidance of genetic pollution risk. Towards this direction, the present study focuses on the feasibility of tropical shrimp species aquaculture in indoor systems evaluating BFT application in temperate zones. The achievability of P. vannamei cultivation inside greenhouses in temperate latitudes is thoroughly examined and a representative experimental biofloc setup for P. vannamei within a greenhouse in Northern Greece is demonstrated. Nevertheless, there are two major limitations, related to economy and ecology, namely the energy demand for high seawater temperature and the fact that most reared shrimps are non-indigenous species setting risk for genetic pollution, respectively. To overcome the former, energy-saving measures such as tank and greenhouse insulation in combination with a microclimate chamber construction were implemented to optimize water temperature at minimal cost. Concerning the latter, there is clear evidence that P. vannamei populations cannot be established in the Mediterranean, setting aside any environmental risk. Overall, based on the developed and tested pilot prototype, employment of optimal management practices, innovative manufacturing and clean energy alternatives, and the utilization of ecosystem services could reduce the environmental impact and maximize the profitability of biofloc operations. These actions could probably permit sustainable and economically viable farming of P. vannamei employing BFT within greenhouses in the Mediterranean. Full article

Vibrio parahaemolyticus is one of the main causative agents leading to acute hepatopancreatic necrosis disease, the severe bacterial disease that occurs during shrimp aquaculture. Hemocytes play important roles during Vibrio infection. Previously, we found that there were few differentially expressed genes (DEGs) between hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before infection. We considered that there should be different immune responses between them after a pathogen infection. Here, the transcriptome data of hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before and after a pathogen infection were compared. The results showed that there were 157 DEGs responsive to infection in V. parahaemolyticus-resistant shrimp, while 33 DEGs in V. parahaemolyticus-susceptible shrimp. DEGs in V. parahaemolyticus-resistant shrimp were mainly related to immune and glycolytic processes, while those in V. parahaemolyticus-susceptible shrimp were mainly related to metabolism, with only two DEGs in common. A further analysis of genes involved in glucose metabolism revealed that GLUT2, HK, FBP, and PCK1 were lowly expressed while PC were highly expressed in hemocytes of the V. parahaemolyticus-resistant shrimp, indicating that glucose metabolism in shrimp hemocytes was related to a V. parahaemolyticus infection. After the knockdown of PC, the expression of genes in Toll and IMD signaling pathways were down-regulated, indicating that glucose metabolism might function through regulating host immunity during V. parahaemolyticus infection. The results suggest that the immune responses between V. parahaemolyticus-resistant and -susceptible shrimp were apparently different, which probably contribute to their different V. parahaemolyticus resistance abilities. Full article

Allergy to shellfishes, including mollusks and crustaceans, is a growing health concern worldwide. Crustacean shellfish is one of the “Big Eight” allergens designated by the U.S. Food and Drug Administration and is the major cause of food-induced anaphylaxis. Shrimp is one of the most consumed crustaceans triggering immunoglobulin E (IgE)-mediated allergic reactions. Over the past decades, the allergen repertoire of shrimp has been unveiled based on conventional immunodetection methods. With the availability of genomic data for penaeid shrimp and other technological advancements like transcriptomic approaches, new shrimp allergens have been identified and directed new insights into their expression levels, cross-reactivity, and functional impact. In this review paper, we summarize the current knowledge on shrimp allergens, as well as allergens from other crustaceans and mollusks. Specific emphasis is put on the genomic information of the shrimp allergens, their protein characteristics, and cross-reactivity among shrimp and other organisms. Full article

Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research. Full article

Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach. Full article

Vibrio parahaemolyticus carrying plasmid encoding toxins PirA and PirB is one of the causative agents leading to the severe disease of AHPND in shrimp aquaculture. However, there is a lack of deep understanding of the host-resistant characteristics against V. parahaemolyticus infection. Here, we established a method to obtain hemocytes from shrimp with different V. parahaemolyticus-resistant abilities and performed comparative transcriptome analysis on the expression profiles at the background level of hemocytes from shrimp in two independent populations. Principal component analysis and sample clustering results showed that samples from the same population had a closer relationship than that from shrimp with similar disease-resistant abilities. DEGs analysis revealed that the number of DEGs between two populations was much more than that between V. parahaemolyticus-resistant and susceptible shrimp. A total of 31 DEGs and 5 DEGs were identified from the comparison between V. parahaemolyticus-resistant and susceptible shrimp from populations 1 and 2, respectively. DEGs from population 1 were mainly cytoskeleton-related genes, metabolic related genes, and immune related genes. Although there was no DEGs overlap between two comparisons, DEGs from population 2 also included genes related to cytoskeleton and metabolism. The data suggest that these biological processes play important roles in disease resistance, and they could be focused by comprehensive analysis of multiple omics data. A new strategy for screening key biological processes and genes related to disease resistance was proposed based on the present study. Full article

Pedigrees are essential components in selective breeding programs to manage genetic diversity and obtain accurate genetic parameter estimates to ensure long-term response to selection in captive populations. High throughput and cost-effective sequencing technologies has offered opportunities of using single nucleotide polymorphisms (SNPs) to resolve penaeid shrimp pedigrees from mass spawning cohorts and communal rearing. Effects of SNPs for sibship assignment were investigated on 546 shrimp using two software programs, Colony and Sequoia. Assignment rates and accuracies using SNP subsets with six different minor allele frequencies (MAFs), four sets of SNPs, and five genotyping error rates were compared to the microsatellite-based pedigree established in a previous study. High MAFs and numbers of SNPs contributed to significant increases in assignment rates and accuracies, whereas genotyping error rates showed negligible impacts on assignment results. Sibship assignments achieved rates and accuracies of 98% and 83%, respectively, with a minimum number of 91 SNPs (average MAF ≥ 0.14), and the two different programs exhibited similar resulting patterns for different SNP subsets. High consistencies between SNP-based and microsatellite-based pedigrees showed that accurate pedigrees could be achieved by using SNPs and thus contribute to the long-term response to selection in farmed banana shrimp. Full article

The outbreaks caused by Vibrio spp. are a notable threat to the potential growth of the economy of penaeid culture, which is still controlled by the administration of antibiotics. At first, the infected group was subjected to phenotypic bacteriological examination with subsequent molecular identification via 16S rRNA gene sequencing, which confirmed four strains of Vibrio spp., V. atlanticus, V. natriegens, V. alginolyticus, and V. harveyi, from moribund-infected shrimp during mortality events in an Egyptian hatchery. To better understand the defense mechanism of the most effective antibiotic against Vibrio strains, the immune responses were compared and evaluated in infected Litopenaeus vannamei broodstock after being fed 5 mg kg⁻¹ of florfenicol antibiotic, which was first determined through in vitro antibiogram tests. Therefore, our study aimed to determine the immune response of L. vannamei during Vibrio spp. infection in Egyptian hatcheries and after antibiotic medication. The parameters assessed were the total and differential hemocyte count (THC), granular cells (GC), semi-granular cells (SGC), and hyaline cells (HC). As well as the metabolic and immune enzymes: alanine aminotransferases (ALT), aspartate aminotransferases (AST), alkaline phosphatase (ALP), acid phosphatase (ACP), and lysozyme activity; an antioxidant index, such as superoxide dismutase (SOD) and glutathione (GSH); a phagocytic assay; changes in reactive oxygen species (ROS); and bactericidal activity in the hemolymph of the control, infected, and treated groups. Further evaluation of the mRNA expression levels of the prophenoloxidase (LvproPO), toll-like receptor 1 (LvToll1), and haemocyanin (LvHc) genes were performed in the hepatopancreas of the same groups. A significant drop in the THC, GC, SGC, and HC counts, as well as lysozyme and bactericidal activities, phagocytic assay, ROS, SOD, and GSH index, were represented in infected shrimp compared to control shrimp; however, a marked increase in the activity of ALT, AST, ALP, and ACP was observed. These activities were significantly restored in the treated shrimp compared to the infected shrimp. Nevertheless, no significant changes were noted in the transcriptional levels of the LvproPO and LvToll1 genes in the treated shrimp when compared to the infected shrimp; however, a significant suppression of the LvHc gene was noted. Our study aimed to determine the immune response of L. vannamei during Vibrio spp. infection in Egyptian hatcheries and after antibiotic medication. We concluded that florfenicol in medicated feed could be effective in controlling vibriosis and ameliorating the immune response of shrimp. Full article

Many environmental and pathogenic insults induce endoplasmic reticulum (ER) stress in animals, especially in aquatic ecosystems, where these factors are crucial for life. In penaeid shrimp, pathogens and environmental stressors induce hemocyanin expression, but the involvement of hemocyanin in ER stress response is unknown. We demonstrate that in response to pathogenic bacteria (Vibrio parahaemolyticus and Streptococcus iniae), hemocyanin, ER stress proteins (Bip, Xbp1s, and Chop), and sterol regulatory element binding protein (SREBP) are induced to alter fatty acid levels in Penaeus vannamei. Interestingly, hemocyanin interacts with ER stress proteins to modulate SREBP expression, while ER stress inhibition with 4-Phenylbutyric acid or hemocyanin knockdown attenuates the expression of ER stress proteins, SREBP, and fatty acid levels. Contrarily, hemocyanin knockdown followed by tunicamycin treatment (ER stress activator) increased their expression. Thus, hemocyanin mediates ER stress during pathogen challenge, which consequently modulates SREBP to regulate the expression of downstream lipogenic genes and fatty acid levels. Our findings reveal a novel mechanism employed by penaeid shrimp to counteract pathogen-induced ER stress. Full article

Gradually, concern for the welfare of aquatic invertebrates produced on a commercial/industrial scale is crossing the boundaries of science and becoming a demand of other societal actors. The objective of this paper is to propose protocols for assessing the Penaeus vannamei welfare during the stages of reproduction, larval rearing, transport, and growing-out in earthen ponds and to discuss, based on a literature review, the processes and perspectives associated with the development and application of on-farm shrimp welfare protocols. Protocols were developed based on four of the five domains of animal welfare: nutrition, environment, health, and behaviour. The indicators related to the psychology domain were not considered a separate category, and the other proposed indicators indirectly assessed this domain. For each indicator, the corresponding reference values were defined based on literature and field experience, apart from the three possible scores related to animal experience on a continuum from positive (score 1) to very negative (score 3). It is very likely that non-invasive methods for measuring the farmed shrimp welfare, such as those proposed here, will become a standard tool for farms and laboratories and that it will become increasingly challenging to produce shrimp without considering their welfare throughout the production cycle. Full article