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The Asian seabass is of importance both as a farmed and wild animal. With the emergence of infectious diseases, there is a need to understand and characterize the immune system. In humans, the highly polymorphic MHC class I (MHC-I) molecules play an important role in antigen presentation for the adaptive immune system. In the present study, we characterized a single MHC-I gene in Asian seabass (Lates calcarifer) by amplifying and sequencing the MHC-I alpha 1 and alpha 2 domains, followed by multi-sequence alignment analyses. The results indicated that the Asian seabass MHC-I α1 and α2 domain sequences showed an overall similarity within Asian seabass and retained the majority of the conserved binding residues of human leukocyte antigen-A2 (HLA-A2). Phylogenetic tree analysis revealed that the sequences belonged to the U lineage. Mapping the conserved binding residue positions on human HLA-A2 and grass carp crystal structure showed a high degree of similarity. In conclusion, the availability of MHC-I α1 and α2 sequences enhances the quality of MHC class I genetic information in Asian seabass, providing new tools to analyze fish immune responses to pathogen infections, and will be applicable in the study of the phylogeny and the evolution of antigen-specific receptors.

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes), most notably Tenacibaculum maritimum. The impact of tenacibaculosis on the fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissues of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farmed fish. The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One isolated strain, TLL-A2T, shares 98.7% 16S rRNA gene identity with Tenacibaculum mesophilum DSM 13764T. The genome of strain TLL-A2T was sequenced and compared to that of T. mesophilum DSM 13764T. Analysis of average nucleotide identity and comparative genome analysis revealed only 92% identity between T. mesophilum DSM 13764T and strain TLL-A2T and differences between the two strains in predicted carbohydrate activating enzymes respectively. Phenotypic comparison between strain TLL-A2T and T. mesophilum DSM 13764T indicated additional differences, such as growth response at different salt concentrations. Based on molecular and phenotypic differences, strain TLL-A2T (=DSM 106434T, KCTC 62393T) is proposed as the type strain of Tenacibaculum singaporense sp. nov.

Asian seabass (or commonly known as barramundi), Lates calcarifer, is a bony euryhaline teleost from the Family Latidae, inhabiting nearshore, estuarine, and marine connected freshwaters throughout the tropical Indo-West Pacific region. The species is catadromous, whereby adults spawn in salinities between 28 and 34 ppt at the mouth of estuaries, with resultant juveniles usually moving into brackish and freshwater systems to mature, before returning to the sea to spawn again as adults. The species lives in both marine and freshwater habitats and can move quickly between the two; thus, the species’ ability to tolerate changes in salinity makes it a good candidate for studying the salinity acclimation response in teleosts. In this study, the transcriptome of two major osmoregulatory organs (gills and kidneys) of young juvenile Asian seabass reared in freshwater and seawater were compared. The euryhaline nature of Asian seabass was found to be highly pliable and the moldability of the trait was further confirmed by histological analyses of gills and kidneys. Differences in major expression pathways were observed, with differentially expressed genes including those related to osmoregulation, tissue/organ morphogenesis, and cell volume regulation as central to the osmo-adaptive response. Additionally, genes coding for mucins were upregulated specifically under saline conditions, whereas several genes important for growth and development, as well as circadian entrainment were specifically enriched in fish reared in freshwater. Routing of the circadian rhythm mediated by salinity changes could be the initial step in salinity acclimation and possibly migration in euryhaline fish species such as the Asian seabass.

Background For Asian seabass ( Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading causes of disease, causing tens of millions of dollars of annual economic losses. Over the years, we conducted farm-based challenges by exposing Asian seabass juveniles to complex natural environmental conditions. In one of these challenges, we collected a total of 1,250 fish classified as either ‘sensitive’ or ‘robust’ individuals during the 28-day observation period. Results We constructed a high-resolution linkage map with 3,089 SNPs for Asian seabass using the double digest Restriction-site Associated DNA (ddRAD) technology and a performed a search for Quantitative Trait Loci (QTL) associated with robustness. The search detected a major genome-wide significant QTL for increased robustness in pathogen-infected marine environment on linkage group 11 (ASB_LG11; 88.9 cM to 93.6 cM) with phenotypic variation explained of 81.0%. The QTL was positioned within a > 800 kb genomic region located at the tip of chromosome ASB_LG11 with two Single Nucleotide Polymorphism markers, R1-38468 and R1-61252, located near to the two ends of the QTL. When the R1-61252 marker was validated experimentally in a different mass cross population, it showed a statistically significant association with increased robustness. The majority of thirty-six potential candidate genes located within the QTL have known functions related to innate immunity, stress response or disease. By utilizing this ddRAD-based map, we detected five mis-assemblies corresponding to four chromosomes, namely ASB_LG8, ASB_LG9, ASB_LG15 and ASB_LG20, in the current Asian seabass reference genome assembly. Conclusion According to our knowledge, the QTL associated with increased robustness is the first such finding from a tropical fish species. Depending on further validation in other stocks and populations, it might be potentially useful for selecting robust Asian seabass lines in selection programs.

Asian Seabass ( Lates calcarifer ) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01 T . Analysis of the strain’s 16S rRNA gene indicates that the strain belongs to the family Vibrionaceae with Photobacterium damselae as its closest relative, albeit sharing only 94.8% (aligned region 1553 bp) nucleotide identity. Comparative genomic analysis with all validly published Vibrionaceae species with available genomes revealed average nucleotide identity (ANI) and DNA–DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01 T , which are well below proposed thresholds for species delineation (ANI, 95–96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the Vibrionaceae family were determined for which strain TLL-SE01 T is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01 T in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01 T and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other Vibrionaceae species, we propose a novel species in a new genus, Parasalinivibrio latis gen. nov. sp. nov. and strain TLL-SE01 T (= BCRC 81435 T  = JCM 36283 T ) as the type strain.

Abstract Canarium indicum offers the potential of usage in aquaculture. This study aimed to evaluate the utilization of C. indicum on growth performance, health, and resistance of Asian seabass Lates calcalifer challenged with Vibrio alginolyticus. The study employed a completely randomized design with seven treatments, namely positive control (K+), negative control (K-), vitamin control (KVit), antibiotic control (KAnt), doses of 5 g kg-1 (D05), 10 g kg-1 (D10), and 20 g kg-1 C. indicum (D20). The test feed was prepared with a coating method and fed for 30 days. On the 31st day of rearing, a challenge test was conducted by injecting V. alginolyticus intramuscularly at 106 CFU mL-1. The results showed that C. indicum treatment for 30 days had a significantly different effect (P<0.05) on weight gain and average daily growth, while KVit and KAnt treatments were not different from the control. After the challenge test, all doses of C. indicum treatment, as well as KVit and KAnt treatments, showed survival significantly different (P<0.05) from that of the positive control, which ranged from 88.89% to 95.56% and was not significantly different (P>0.05) from the negative control. The survival rate condition is identical to the cumulative survival condition which shows the highest mortality found in the positive control. The administration of C. indicum at a dose of 5 g kg-1 to 20 g kg-1 improved the growth performance and prevented V. alginolyticus infection. Highlight Research C. indicum significantly increases the growth of Asian seabass. C. indicum significantly enhances the immune response to V. alginolyticus infection in Asian seabass. C. indicum can prevent V. alginolyticus infection as it resulted in a higher and cumulative survival than the positive control. C. indicum can be developed as an immunostimulant for the prevention of vibriosis in Asian seabass at doses of 5 g kg-1 to 20 g kg-1.

This study aims to estimate the economic loss due to vibriosis in the production of Asian seabass in floating net-cages on the east coast of Peninsular Malaysia. Asian seabass has contributed significantly to Malaysia's economic activities and food security. However, its production can be hindered by the occurrence of diseases, such as vibriosis, causing severe economic losses to farmers. A questionnaire-based survey was conducted on 14 small-scale monoculture Asian seabass net-cage farms. Using a stochastic bioeconomic model and inputs from the survey, existing literature, and expert opinion, the economic losses were determined. Moreover, this model considered the prevalence of Vibrio spp. at a farm on the east coast and the risk posed by its infection from hatcheries. The results showed that 71.09% of Asian seabass simulated in the stochastic model survived. The mortality rate due to vibriosis and other causes was at 16.23 and 12.68%, respectively. The risk posed by Vibrio spp. infection from hatcheries contributed to 2.77% of the increase in Asian seabass mortality. The stochastic model estimated that the total cost of producing a tail of Asian seabass was €2.69 per kilogram. The economic loss of vibriosis was estimated at €0.19 per tail per kilogram, which represents 7.06% of the total production cost of Asian seabass per kilogram. An increase in the prevalence of clinical vibriosis and vibriosis case fatality rate at 42 and 100%, respectively, will lead to an increase in the cost of grow-out Asian seabass by €0.29 per tail from the default value. An increase in pellet price per kilogram by €1.38 and feed conversion ratio pellet by 0.96 will consequently increase the cost of grow-out Asian seabass by €2.29 per tail and €0.82 per tail, respectively. We find that the occurrence of Vibrio spp. infection at the hatchery level can contribute to an increased risk in the mortality of Asian seabass during the grow-out phase. Hence, we also need to focus on the control and prevention of vibriosis infection from hatcheries.

In the present study, chitosan-based bivalent nanovaccines of S. iniae and F. covae were administered by immersion vaccination at 30 and 40 days after hatching (DAH), and the third vaccination was orally administered by feeding at 50 DAH. ELISA revealed that the levels of total IgM and specific IgM to S. iniae and F. covae were significantly elevated in all vaccinated groups at 10, 20, and 30 days after vaccination (DAV). A qRT-PCR analysis of immune-related genes revealed significantly higher IgT expression in the vaccinated groups compared to the control group, as revealed by 44–100-fold changes in the vaccinated groups compared to the control (p < 0.001) at every tested time point after vaccination. All vaccinated groups expressed IgM, MHCIIα, and TCRα at significantly higher levels than the control group at 10 and/or 20 DAV (p < 0.05). In the S. iniae challenge tests, the survival of vaccinated groups ranged from 62.15 ± 2.11 to 75.70 ± 3.36%, which significantly differed from that of the control group (44.44 ± 1.92%). Similarly, all vaccinated groups showed higher survival rates of 68.89 ± 3.85 to 77.78 ± 5.09% during F. covae challenge than the control groups (50.00 ± 3.33%) (p < 0.05).

Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), is one major threat to mariculture. Identifying loci and understanding the mechanisms associated with resistance to VNN are important in selective breeding programs. We performed a genome-wide association study (GWAS) using genotyping-by-sequencing (GBS) to study the genomic architecture of resistance to NNV infection in Asian seabass. We genotyped 986 individuals from 43 families produced by 15 founders with 44498 bi-allelic genetic variants using GBS. The GWAS identified three genome-wide significant loci on chromosomes 16, 19, and 20, respectively, and six suggestive loci on chromosomes 1, 8, 14, 15, 21, and 24, respectively, associated with resistance to NNV infection measured as binary and quantitative traits. Using the 500 most significant markers in combination with a training population of 800 samples could reach a genomic prediction accuracy of 0.7. Candidate genes significantly associated with resistance to NNV, including lysine-specific demethylase 2A, beta-defensin 1, and cystatin-B, which play important roles in immune responses against virus infection, were identified. Almost all the candidate genes were differentially expressed in different tissues against NNV infection. The significant genetic variants can be used in genomic selection and help understand the mechanism of resistance to VNN. Future studies should use populations of large effective size and whole genome resequencing to identify more useful genetic variants.

Asian seabass (Lates calcarifer ) is becoming an important species for aquaculture. However, the Asian seabass aquaculture industry faces a significant challenge of disease outbreaks that can jeopardize fish health and production. This review delves into the major diseases affecting Asian seabass aquaculture and explores their causes, symptoms, and management approaches. We focused on the key pathogens responsible for these outbreaks, the environmental factors contributing to disease susceptibility, and the latest advancements in disease prevention and management. By addressing these critical aspects, this review addresses the needs of aquaculturists, researchers, and policymakers with the knowledge required to promote resilient and sustainable Asian seabass farming. We aim to shed light on the challenges posed by disease while highlighting innovative strategies that offer promise for the future of this thriving industry. This comprehensive examination serves as a valuable resource for those invested in ensuring the health and vitality of Asian seabass, securing a consistent supply to meet the demands of global seafood markets.