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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]

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]

'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]

Marine farming of barramundi (Lates calcarifer) in Southeast Asia is currently severely affected by viral diseases. To better understand the biological implications and gene expression response of barramundi in commercial farming conditions during a disease outbreak, the presence of pathogens, comparative RNAseq, and histopathology targeting multiple organs of clinically "sick" and "healthy" juveniles were investigated. Coinfection of scale drop disease virus (SDDV) and L. calcarifer herpes virus (LCHV) were detected in all sampled fish, with higher SDDV viral loads in sick than in healthy fish. Histopathology showed that livers in sick fish often had moderate to severe abnormal fat accumulation (hepatic lipidosis), whereas the predominant pathology in the kidneys shows moderate to severe inflammation and glomerular necrosis. The spleen was the most severely affected organ, with sick fish presenting severe multifocal and coalescing necrosis. Principal component analysis (PC1 and PC2) explained 70.3% of the observed variance and strongly associated the above histopathological findings with SDDV loads and with the sick phenotypes, supporting a primary diagnosis of the fish being impacted by scale drop disease (SDD). Extracted RNA from kidney and spleen of the sick fish were also severely degraded likely due to severe inflammation and tissue necrosis, indicating failure of these organs in advanced stages of SDD. RNAseq of sick vs. healthy barramundi identified 2,810 and 556 differentially expressed genes (DEGs) in the liver and muscle, respectively. Eleven significantly enriched pathways (e.g., phagosome, cytokine-cytokine-receptor interaction, ECM-receptor interaction, neuroactive ligand-receptor interaction, calcium signaling, MAPK, CAMs, etc.) and gene families (e.g., tool-like receptor, TNF, lectin, complement, interleukin, chemokine, MHC, B and T cells, CD molecules, etc.) relevant to homeostasis and innate and adaptive immunity were mostly downregulated in sick fish. These DEGs and pathways, also previously identified in L. calcarifer as general immune responses to other pathogens and environmental stressors, suggest a failure of the clinically sick fish to cope and overcome the systemic inflammatory responses and tissue degeneration caused by SDD. [ABSTRACT FROM AUTHOR]

Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer , Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls. [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]

Ischemic stroke is the second leading cause of death worldwide. Ischemia-induced cognitive dysfunction may result in a poor quality of life. Synaptic plasticity plays a key role in cognition promotion. An enriched environment (EE), which can attenuate cognitive deficits in chronic cerebral hypoperfusion, has been shown to facilitate synaptic plasticity. However, the effect of EE on synaptic plasticity in bilateral cerebral hemispheres in stroke remains unclear. This study used a permanent middle cerebral artery occlusion mouse model, which was divided into standard housing and EE groups. The Morris water maze test was performed to detect the cognitive function. Electron microscopy was used to determine the synapse numbers. The expression of SYN and GAP-43 was then quantified by immunofluorescence staining and Western blot analysis. Compared with the standard housing, EE promoted the cognitive function recovery in the mice with stroke. Moreover, EE increased the synapse numbers and the expression of SYN and GAP-43 in both the ipsilateral and contralateral hemispheres (P < 0.05). A further correlation analysis revealed a positive correlation between the cognitive function outcomes and the relative expression of GAP-43 and SYN. Furthermore, the correlation of the expression of GAP-43 and SYN with cognitive function was higher in the contralateral brain than in the ipsilateral brain. In conclusion, an EE may promote cognitive function via bilateral synaptic remodeling after cerebral ischemia. Also, the contralateral brain may play an important role in the recovery of cognitive function. [ABSTRACT FROM AUTHOR]

Brain has limited capacity for spontaneous recovery of lost function after stroke. Exposure to enriched environment (EE) can facilitate functional recovery, but mechanisms underlying this effect are poorly understood. Here, we used a middle cerebral artery occlusion (MCAO) model to investigate the impact of EE on angiogenesis in the post-ischemic brain in adult male Sprague Dawley rats, and examined whether blood-borne factors may contribute. Compared with standard cage (SC), exposure to EE was associated with greater improvement in neurological function, higher peri-infarct vascular density, and higher chronic post-ischemic cerebral blood flow assessed by laser speckle imaging. The effect persisted for at least 28 days. EE also enhanced the expression of hepatocyte growth factor in the peri-ischemic cortex when measured 15 days after MCAO. Interestingly, serum from rats exposed to EE after MCAO showed elevated levels of hepatocyte growth factor, and plasma or serum from rats exposed to EE after MCAO enhanced the survival and proliferation of cultured endothelial cells, in vitro, when compared with control plasma or serum from SC group after MCAO. Together, our data suggest that exposure to EE promotes angiogenesis in the ischemic brain that may in part be mediated by blood-borne factors. [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]

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]

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Sex determination and sex differentiation are important phenomena in fish, but the mechanisms of sex determination in Takifugu rubripes are poorly understood. In our study, the expression patterns of genes for DMRTs ( DMRT1, DMRT2 and DMRT3), sox9 a and sox9 b in T. rubripes tissues were verified with the Reverse Transcription (RT)-PCR detection. It is showed that DMRT1 expressions in testis and ovaries were much lower, and no expressions were found in muscle, blood and tailfin. However, expressions for DMRT2 and DMRT3 were not found in the tissues stated above. Transcripts of sox9 a were detected in muscle, fin, ovary and testis, but not in blood, whereas sox9 b expression was only detected in ovary. The expression patterns of DMRTs, sox9 a and sox9 b in T. rubripes gonads suggest that these genes may not be sex-specific. [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.

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]