The State of "Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

Insights into molecular aspects of pathogenesis and disease management in acute hepatopancreatic necrosis disease (AHPND): An updated review

Shrimp aquaculture is a rapidly growing sector that makes a significant economic contribution. However, the aquaculture industry is confronted with significant challenges, and infectious diseases, notably Acute Hepatopancreatic Necrosis Disease (AHPND), have emerged as severe threat. AHPND is caused by pathogens carrying the pVA-1 plasmid, which expresses the PirAB toxin, and it has wreaked havoc in shrimp aquaculture, imposing substantial economic burdens. To address this issue, it is crucial to delve into shrimp's immune responses. Therefore, this comprehensive review offers an in-depth examination of AHPND outbreaks, encompassing various facets such as environmental factors, host susceptibility, and the mechanisms employed by the pathogens. Traditional approaches to combat AHPND, primarily relying on chemicals and antibiotics, have raised concerns related to antibiotic resistance and have demonstrated limited success in disease control. Hence this review spotlights recent advancements in molecular diagnostics, therapeutic agents, and research related to shrimp immunity. Understanding these developments is crucial in the ongoing battle against AHPND. In conclusion, this review underscores the pressing need to comprehend the underlying mechanisms of AHPND pathogenesis and emphasizes the importance of developing comprehensive and effective solutions to combat this devastating disease, which continues to threaten the sustainability of shrimp farming.

Multiomics Analysis-Based Biomarkers in Diagnosis of Polycystic Ovary Syndrome

Polycystic ovarian syndrome is an utmost communal endocrine, psychological, reproductive, and metabolic disorder that occurs in women of reproductive age with extensive range of clinical manifestations. This may even lead to long-term multiple morbidities including obesity, diabetes mellitus, insulin resistance, cardiovascular disease, infertility, cerebrovascular diseases, and ovarian and endometrial cancer. Women affliction from PCOS in midst assemblage of manifestations allied with menstrual dysfunction and androgen exorbitance, which considerably affects eminence of life. PCOS is recognized as a multifactorial disorder and systemic syndrome in first-degree family members; therefore, the etiology of PCOS syndrome has not been copiously interpreted. The disorder of PCOS comprehends numerous allied health conditions and has influenced various metabolic processes. Due to multifaceted pathophysiology engaging several pathways and proteins, single genetic diagnostic tests cannot be supportive to determine in straight way. Clarification of cellular and biochemical pathways and various genetic players underlying PCOS could upsurge our consideration of pathophysiology of this syndrome. It is requisite to know pathophysiological relationship between biomarker and their reflection towards PCOS disease. Biomarkers deliver vibrantly and potent ways to apprehend the spectrum of PCOS with applications in screening, diagnosis, characterization, and monitoring. This paper relies on the endeavor to point out many candidates as potential biomarkers based on omics technologies, thus highlighting correlation between PCOS disease with innovative technologies. Therefore, the objective of existing review is to encapsulate more findings towards cutting-edge advances in prospective use of biomarkers for PCOS disease. Discussed biomarkers may be fruitful in guiding therapies, addressing disease risk, and predicting clinical outcomes in future.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.

Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G₀) were ranked on genomic breeding values for WSSV resistance. Two G₁ populations were produced, one from G₀ breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G₁) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Background

The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).

Results

Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.

Conclusion

Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

The biology and ecology of the banana prawns: Penaeus merguiensis de Man and P. indicus H. Milne Edwards

The two banana prawns Penaeus merguiensis and P. indicus are arguably the most commercially important species of penaeid prawns in the tropical and sub-tropical Indo-West Pacific region. They are fecund, short-lived, and have a complex life history involving offshore spawning, inshore mangrove-lined nursery grounds, and migrations between the two locations. We have reviewed and assessed published research on: the fisheries and aquaculture; taxonomy and identification; distribution and habitat preferences; growth; mortality; food and feeding; predation, and the importance of the mangrove habitat to banana prawns. We have examined the life history patterns of these two banana prawns and the many environmental and biological factors that affect different life history stages, often resulting in large interannual variations in abundances of adult prawns and commercial catches. We have also reviewed research on the ecosystem relationships involving these prawns, including fishery impacts on the environment and other species caught as bycatch. In reviewing the published information on factors affecting recruitment dynamics and variability, we have sometimes found contrasting and confounding results, suggesting that these factors are not yet fully understood. Therefore, for each aspect of the prawns' biology we have pointed to areas with incomplete or conflicted understanding, which will hopefully guide future research on these extremely valuable prawn species.

Evaluating antimicrobial resistance in the global shrimp industry

Antimicrobial resistance (AMR) is a growing threat to global public health, and the overuse of antibiotics in animals has been identified as a major risk factor. With high levels of international trade and direct connectivity to the aquatic environment, shrimp aquaculture may play a role in global AMR dissemination. The vast majority of shrimp production occurs in low- and middle-income countries, where antibiotic quality and usage is widely unregulated, and where the integration of aquaculture with family livelihoods offers many opportunities for human, animal and environmental bacteria to come into close contact. Furthermore, in shrimp growing areas, untreated waste is often directly eliminated into local water sources. These risks are very different to many other major internationally-traded aquaculture commodities, such as salmon, which is produced in higher income countries where there are greater levels of regulation and well-established management practices. Assessing the true scale of the risk of AMR dissemination in the shrimp industry is a considerable challenge, not least because obtaining reliable data on antibiotic usage is very difficult. Combating the risks associated with AMR dissemination is also challenging due to the increasing trend towards intensification and its associated disease burden, and because many farmers currently have no alternatives to antibiotics for preventing crop failure. In this review, we critically assess the potential risks the shrimp industry poses to AMR dissemination. We also discuss some of the possible risk mitigation strategies that could be considered by the shrimp industry as it strives for a more sustainable future in production.

Lipidomics biomarkers in women with polycystic ovary syndrome (PCOS) using ultra-high performance liquid chromatography-quadrupole time of flight electrospray in a positive ionization mode mass spectrometry

Polycystic ovary syndrome (PCOS), characterized by oligo-anovulation and androgen excess is considered a high-risk condition for metabolic disorders. Herein, untargeted metabolomics analysis was applied to women with PCOS, aiming to provide deeper insights into lipidomics biomarkers signature of PCOS, for better diagnosis and management. This was a cross-sectional study in which 15 Caucasian women with PCOS and 15 Caucasian healthy, age-matched women were enrolled. Lipidomics analysis was performed using Ultra-High Performance Liquid Chromatography-Quadrupole Time of Flight Electrospray Mass Spectrometry. Partial Least Squares Discriminant Analysis retrieved the most important discriminative metabolites. Significantly increased levels of triacylglycerol (18:2/18:2/0-18:0) in addition to cholestane-3beta, 5alpha, 6beta-triol (18:0/0:0) and cholestane-5alpha (18:1/0:0) appeared as valuable variables to differentiate subjects with PCOS from controls. Acyl-carnitine 2-hydroxylauroylcarnitine was significantly elevated in PCOS in opposition to decreased phosphocholines metabolites (18:1/18:4, 18:3/18:2), to suggest a metabolic pattern linked to lipid peroxidation. A high fat intake or reduced fat energy consumption during nighttime due to diminished ability to switch to lipid oxidation during fasting time possibly contribute to hypertriglyceridemia found in PCOS. Furthermore, inflammatory mediators including metabolites of the prostaglandin (PG) E2 pathway and oxo-leukotrienes (LT) were increased in patients with PCOS. Potential lipidomics biomarkers were identified that could stratify between women with PCOS and healthy controls. The results show particular alterations in acylglycerols, PGs and LTs and phosphocholines and carnitine metabolites. The lipidomics profiles of PCOS indicate a higher risk of developing metabolic diseases.

Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production

Omics-technologies have revolutionized biomedical research over the past two decades, and are now poised to play a transformative role in aquaculture. This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (CBPD), with the objective to showcase the state-of-the-science for Omics in aquaculture. In this editorial, we describe the role that Omics can play in aquaculture, and provide a synopsis for each of the Special Issue articles that use these technologies to improve aquaculture practices. Current genomic resources available for some aquaculture species are also described. The number of datasets is impressive for species such as Atlantic salmon and rainbow trout, totaling in the thousands (NCBI Gene Expression Omnibus and Sequence Read Archive). We present a conceptual framework that describes how Omics can be leveraged to understand complex responses of aquatic animals in culture for relevant physiological outcomes, such as fecundity, growth, and immunity. Lastly, knowledge gaps and new directions are identified to address current obstacles in aquaculture. Articles in this Special Issue on aquaculture in CBPD highlight the diversity and scope of Omics in aquaculture. As the technology becomes more cost-effective, it is anticipated that genomics, transcriptomics, proteomics, metabolomics and lipidomics will play increasingly important roles in stock diagnostics (e.g. genetics, health, performance). The timing is right, as global concerns are reaching critical levels over food availability/security and water restrictions for humankind.

Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries.

Thymosins participate in antibacterial immunity of kuruma shrimp, Marsupenaeus japonicus

Thymosins β are actin-binding proteins that play a variety of different functions in inflammatory responses, wound healing, cell migration, angiogenesis, and stem cell recruitment and differentiation. In crayfish, thymosins participate in antiviral immunology. However, the roles of thymosin during bacterial infection in shrimp remain unclear. In the present study, four thymosins were identified from kuruma shrimp, Marsupenaeus japonicus, and named as Mjthymosin2, Mjthymosin3, Mjthymosin4, and Mjthymosin5 according the number of their thymosin beta actin-binding motifs. Mjthymosin3 was selected for further study because its expression level was the highest in hemocytes. Expression analysis showed that Mjthymosin3 was upregulated in hemocytes after challenged by Vibrio anguillarum or Staphylococcus aureus. The recombinant Mjthymosin3 protein could inhibit the growth of certain bacteria in an in vitro antibacterial test. Mjthymosins could facilitate external bacterial clearance in shrimp, and were beneficial to shrimp survival post V. anguillarum or S. aureus infection. The results suggested that Mjthymosins played important roles in the antibacterial immune response of kuruma shrimp.