Search

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. [ABSTRACT FROM AUTHOR]

Diseases caused by pathogens commonly occurring in the aquatic environment or those that are non‐host specific are prevalent and threaten the rapid growth of tropical aquaculture. This study investigates causes of mortality in 12 batches of newly stocked juvenile Lates calcarifer from three different hatcheries. Cytology based on Diff‐Quik™‐stained tissue and blood smears provides rapid diagnosis of possible causes of mortality, while histopathology and haematology provide a better understanding of how prolonged transport and fish with existing chronic disease are more likely to experience elevated mortality post‐stocking. Our findings showed that accumulation of ammonia during prolonged transport causes extensive damage to epithelial barriers in gastrointestinal tracts and depressed immunity due to marked hypoglycaemia, predisposing fish to acute Streptococcosis. Lates calcarifer with chronic bacterial enteritis developed severe hypoglycaemia, had low circulating total plasma protein, and suffered high mortality within 24 hours post‐stocking. Hypoglycaemia and low circulating blood proteins disrupt osmoregulation and exacerbate dehydration, which is fatal in fish in sea water. Dying L. calcarifer tested PCR positive for scale drop disease virus (SDDV) at 28 days post‐stocking showed a 10‐fold elevation of white blood cell counts, severe vasculitis, and obstruction of blood supply to major organs. Destruction of important immune organs such as spleen is a hallmark of SDDV infection that explains high incidences of opportunistic Vibrio harveyi infections in 61% of fish with SDDV. Overall, this study reiterates the importance of stocking disease‐free fish and reducing transport stress. [ABSTRACT FROM AUTHOR]

An enriched environment (EE) has been demonstrated to improve functional recovery in animal models of ischaemic stroke through enhancing vascular endothelial growth factor- (VEGF-) mediated neuroprotection accompanied by angiogenesis in the ischaemic hemisphere. Whether EEs also promote VEGF-mediated neuroprotection and angiogenesis in the contralateral hemisphere remains unclear. Here, we explored the effect of EEs on VEGF expression and angiogenesis within the contralateral cerebral cortex in a rat middle cerebral artery occlusion/reperfusion (MCAO/r) model. We assessed the expression levels of platelet endothelial cell adhesion molecule-1 (CD31), VEGF, and endothelial nitric oxide synthase (eNOS) in the whole contralateral cerebral cortex using Western blotting assay but did not find an increase in the expression of CD31, VEGF, or eNOS in MCAO/r rats housed in EEs, which suggested that EEs did not enhance the overall expression of VEGF and eNOS or angiogenesis in the entire contralateral cortex. We further analysed the local effect of EEs by immunohistochemistry and found that in and around the bilateral cingulum in MCAO/r rats housed in EEs, haematopoietic progenitor cell antigen- (CD34-) positive endothelial progenitor cells were significantly increased compared with those of rats housed in standard cages (SCs). Further experiments showed that EEs increased neuronal VEGF expression surrounding the cingulum in MCAO/r rats and robustly upregulated eNOS expression. These results revealed that EEs enhanced angiogenesis, VEGF expression, and activation of the VEGF-eNOS pathway in and/or around the cingulum in MCAO/r rats, which were involved in the functional recovery of MCAO/r rats. [ABSTRACT FROM AUTHOR]

The farming of several species in aquaculture often produces pale coloured fish due to a deficiency in dietary carotenoid sources compared to their wild caught counterparts, resulting in the loss of market value and consumer acceptance. Supplementation of feed with astaxanthin as a carotenoid source has since been found to enhance red colouration in several important fish species. In this study, comparative transcriptome analysis was performed on the skin from the main body (dorsolateral region) and caudal fin of Malabar snappers (Lutjanus malabaricus) fed with and without astaxanthin over a 32-day period to identify genes related to the trait. All clean reads were assembled into 205,940 unigenes with a N50 of 2079 bp. A total of 881 and 178 differentially expressed genes (DEGs) between Control Body (CB) vs Treatment Body (TB) and Control Fin (CF) vs Treatment Fin (TF) were identified respectively, where expression patterns suggested that pigment-related genes bco1 , bco2l , pax7 , slc7a11 , hsp70, and stard5 are key genes involved in the enhancement of red colouration in Malabar snappers. Metabolic pathways related to pigmentation such as PI3k-Akt, MAPK, Wnt, cAMP, and Ras signaling are likely to play vital roles in the enhancement of red colouration in juvenile Malabar snappers. In addition, numerous immune-related genes were found to be differentially expressed for both CB vs TB and CF vs TF, suggesting the potential use of dietary astaxanthin as an immunostimulant. The present study provides a foundation to the understanding of the molecular mechanisms involved in carotenoid-induced colouration, and development of breeding and culture practices to produce farmed Malabar snappers with the desired consumer-favoured traits. • Comparative transcriptome of skin from body and caudal fin of Lutjanus malabaricus fed with and without astaxanthin. • Key genes and pathways related to red pigmentation identified in astaxanthin-fed Malabar snappers. • Dietary astaxanthin as potential immunostimulant. • This study provides insights into the further understanding of red pigmentation in L. malabaricus [ABSTRACT FROM AUTHOR]

Members of the Fox gene family of transcriptional regulators are essential for animal development and have been extensively studied in vertebrates. The mouse and human genomes contain at least 40 FOX genes which are divided into 19 subclasses based on the sequence similarity of the highly conserved forkhead domain. Using the genome sequence of the Takifugu rubripes and Tetraodon nigroviridis, we examined the genomic complement of fox genes in these organisms to gain insight into the evolutionary relationship of this gene family. We identified 53 fox genes in Tetraodon nigroviridis and Takifugu rubripes genome by searching the forkhead domain. These genes are divided into 18 subclasses as follows: 8 fox genes in subclass O; 6 in subclass P ; 4 in subclasses D, J, and N; 3 in subclasses A, B, C, E, F, and I; 2 in subclasses K, L, and Q; and 1 in subclasses G, H, M, and R. Together with the forkhead domain sequences of human, chicken, frog, zebrafish, medaka, and Caenorhabditis elegans, the phylogenetic relationship of the fox genes in Takifugu rubripes and Tetraodon nigroviridis were analyzed and compared. The genes structure, general features, and the three-dimensional model of these genes were also discussed. [ABSTRACT FROM AUTHOR]

Abstract: Estrogen and androgen and their receptors play critical roles in physiological processes such as sexual differentiation and development. Using the available structural models for the human estrogen receptors alpha and beta and androgen receptor as templates, we designed in silico agonist and antagonist models of medaka estrogen receptor (meER) alpha, beta-1, and beta-2, and androgen receptor (meAR) alpha and beta. Using these models, we studied (1) the structural relationship between the ligand-binding domains (LBDs) of ERs and ARs of human and medaka, and (2) whether medaka ER and AR can be potential models for studying the ligand-binding activities of various agonists and antagonists of these receptors by docking analysis. A high level of conservation was observed between the sequences of the ligand-binding domains of meERα and huERα, meERβ1 and huERβ, meERβ2, and huERβ with 62.8%, 66.4%, and 65.1% identity, respectively. The sequence conservation between meARα and huAR, meARβ, and huAR was found with 70.1% and 61.0% of identity, respectively. Thirty-three selected endocrine disrupting chemicals (EDCs), including both agonists and antagonists, were docked into the LBD of ER and AR, and the corresponding docking score for medaka models and human templates were calculated. In order to confirm the conservation of the overall geometry and the binding pocket, the backbone root mean square deviation (RMSD) for Cα atoms was derived from the structure superposition of all 10 medaka homology models to the six human templates. Our results suggested conformational conservation between the ERs and ARs of medaka and human, Thus, medaka could be highly useful as a model system for studies involving estrogen and androgen interaction with their receptors. [Copyright &y& Elsevier]

Abstract: Genetic linkage maps of guppy (Poecilia reticulata) were constructed using microsatellite DNA and AFLP markers and a pseudo-testcross mapping strategy. (AC)n microsatellite DNA markers were developed and used to genotype sixty-one full-sib progenies (F1) and their two parents. Of 293 microsatellite DNA markers, 101 segregated at 1:1 or 1:1:1:1 ratios. In addition, 336 AFLP markers segregated also in F1 progenies at 1:1 ratio, which were produced using 91 primer combinations. All these markers were mapped with two linkage maps produced, one each parent. Female map included 135 markers in 22 linkage groups, covering a total of 1267.7 cM in length. Male map included 172 markers in 20 linkage groups, covering a total of 1771.2 cM in length. [Copyright &y& Elsevier]

Malabar red snapper (Lutjanus malabaricus) is an important and high-value aquaculture species in Singapore that is attracting substantial interest and new industry investment. The consistent production of good quality eggs is an important step for establishing a selective breeding program for the species in Singapore. To achieve improved spawning outcomes, reproductive studies are needed to address the challenges in Malabar red snapper seed production, such as limited spawning success in closed culture systems. However, despite its rising profile as an aquaculture candidate and the need to improve broodstock husbandry, currently there are scarce genomic resources for the species, particularly related to genes involved in sex determination and differentiation. Herein, we report the first gonadal transcriptomes of adult L. malabaricus generated using RNA-Seq of testes (n = 6) and ovaries (n = 6). A total of 14,421 significant differentially expressed genes (DEGs) were found by comparing the gene expression profiles of ovaries and testes, including 6499 upregulated female-biased and 7922 downregulated male-biased DEGs. These DEGs included genes known to be involved in reproductive processes such as male-biased dmrt1, spat4, odf3b and sox9, and female-biased cyp19a1, zp4, sox3, bmp15 and esr1. The expression level of 16 selected DEGs were validated by RT-qPCR. This study lays the basis for further research in genes involved in sex determination and differentiation, sex control and breeding in Malabar red snapper. • L. malabaricus is an important aquaculture species in Singapore and the region. • RNA-Seq was performed on testes and ovaries of adult Malabar red snapper (MRS). • We report the first gonad transcriptome of MRS for both sexs with 14,421 DEGs. • This work lays the basis for further research in MRS gonad development. [ABSTRACT FROM AUTHOR]

The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was screened using 22 SSR markers located on linkage group 2 which contains a growth-related QTL region. Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 187 sequences covering 9.7 Mb. Eleven genes annotated within this region were found to be potentially associated with growth and their tissue-specific expression was investigated. Correlation analysis demonstrated that SNPs in ctsb, skp1 and ppp2ca can be potentially used as markers for selecting fast-growing fingerlings. Conserved syntenies between seabass LG2 and five other teleosts were identified. This study i) provided a 10 Mb targeted genome assembly; ii) demonstrated NGS of BAC pools as a potential approach for mining candidates underlying QTLs of this species; iii) detected eleven genes potentially responsible for growth in the QTL region; and iv) identified useful SNP markers for selective breeding programs of Asian seabass. [ABSTRACT FROM AUTHOR]

As nutrition-related expenses constitute the majority of the costs for aquaculture farms, it is essential for them to use feeds that provide an ideal combination of nutrients for the species of choice. In this study, the relative effect of consuming three different pelleted feeds (B, C and D) in comparison to frozen baitfish (A; control) were compared on juvenile Asian seabass (77.3 ± 22.4g) that were selected for increased growth rate over two generations. Our objectives were: 1) to evaluate the effects of different pelleted feeds based on overall physiological changes and nutritional quality of fillets; 2) improve our understanding of the underlying mechanisms with transcriptomic analysis; 3) if possible, identify the feed type that supports the growth of these fishes without substantially reducing the nutritional quality of fillet. The growth performance, fatty acid composition of fillet, hepatic histology and transcriptome of the fishes (Groups A-D) were analyzed. The majority of fatty acids of the fillets, except γ-linolenic acid (GLA, C18:3n6), correlated significantly with the respective diets. Asian seabass fed Feed C showed highest specific growth rate (SGR) and feed conversion efficiency (FCE) with closest histology and transcriptomic profile to control, but their fillet contained the highest n6/n3 ratio. When the liver-based transcriptomes were analyzed, a complex set of differentially expressed genes were detected between groups fed pelleted feeds and controls as well as among the pellet-fed groups themselves. Significant enrichment of genes with growth-related function tallied with the morphological data measured. When compared with control (Group A), ‘Biosynthesis of unsaturated fatty acids’ and ‘Steroid biosynthesis’ pathways were significantly enriched in pellet-fed groups. Reduced goblet cell numbers were observed in the gut of pellet-fed fish compared to controls and fads6 was found to be a suitable candidate gene to separate wild-caught Asian seabass, from pellet-fed ones. These results provide insights for researchers on the various effects of feeds on the biochemistry and global gene expression of the fish and potentially for seabass farms to make more informed feed choices. [ABSTRACT FROM AUTHOR]

'Big belly' disease is a chronic, granulomatous bacterial enteritis and peritonitis, first reported in 3‐ to 4‐week‐old Asian seabass or barramundi, Lates calcarifer Bloch fry. Affected fry are emaciated and have a swollen abdomen, and the condition is referred to as 'skinny pot‐belly' or 'big belly' disease. In this study, histopathological examinations of diseased fish from a batch of 2‐month‐old, 6‐ to 8‐cm L. calcarifer fingerlings, kept in seawater recirculating aquaculture systems, showed pathology resembling 'big belly' disease. Ethanol‐fixed tissues were tested positive using specific PCR primers based on 16S rRNA genes. In situ hybridization using dioxygenin‐labelled positive PCR products on formalin‐fixed paraffin‐embedded tissues showed positive reactions with intralesional, clusters of the large, 'big belly' coccobacilli. A phylogenetic tree constructed based on analyses of these 16S rRNA gene PCR products from five positive fish suggests that the 'big belly' bacterium is most likely a novel Vibrio species. [ABSTRACT FROM AUTHOR]

Asian seabass (Lates calcarifer) is a major aquaculture food fish species in Singapore. Farming of this species is increasingly threatened by frequent outbreaks of infectious diseases, resulting in mortality exceeding 50–70%. In this study, we investigated the comparative gut bacterial microbiota using 16S rRNA metasequencing between asymptomatic and diseased juvenile fish collected during a disease outbreak soon after stocking. Mild to severe chronic granulomatous enteritis was observed histopathologically in both asymptomatic and diseased fish. Kidneys of diseased fish tested PCR positive for the 'big belly' novel Vibrio spp., Streptococcus iniae and Vibrio harveyi. These bacteria were also readily detected by PCR in water samples corresponding to tanks fish were sampled from. Potentially beneficial microbes that promote gut health such as Firmicutes , Bacteroidota and Actinobacteriota were the dominant phyla in the intestinal microbiota of asymptomatic fish. Moreover, the bacteria with probiotic potential such as Lactobacillus only presented in asymptomatic fish, and Weissella was unique and prevalent (47.59%) in asymptomatic fish during the recovery phase of the disease outbreak, making them candidate biomarkers for monitoring health status of L. calcarifer. Conversely, diseased fish showed reduced diversity of their gut microbiome, with high abundance of members of the phylum Proteobacteria. Vibrio was the most dominant genus (87.3%) and Streptococcus iniae was only detected in diseased fish. These findings provide a baseline study for understanding changes in intestinal microbiota in newly stocked fish with mixed bacterial infection, biomarker assisted health monitoring, and future host-derived probiotics screening in L. calcarifer. • This study provides a baseline for understanding changes in gut microbiome in newly stocked L. calcarifer with mixed bacterial infections. • 'Big belly' novel Vibrio spp., Streptococcus iniae and Vibrio harveyi , were detected in only one asymptomatic L. calcarifer , but all diseased fish. • Gut microbiota in diseased fish was dominated by Vibrio. • Unique presence of Weissella and Lactobacillus in asymptomatic fish has potential as biomarkers assisted health monitoring in L. calcarifer. [ABSTRACT FROM AUTHOR]

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics. [ABSTRACT FROM AUTHOR]

A correction to the article "Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding" that was published in the previous issue, is presented.