Current status of research on aquaculture genetics and genomics-information from ISGA 2018

Advances in Vibrio-related infection management: an integrated technology approach for aquaculture and human health

Vibrio species pose significant threats worldwide, causing mortalities in aquaculture and infections in humans. Global warming and the emergence of worldwide strains of Vibrio diseases are increasing day by day. Control of Vibrio species requires effective monitoring, diagnosis, and treatment strategies at the global scale. Despite current efforts based on chemical, biological, and mechanical means, Vibrio control management faces limitations due to complicated implementation processes. This review explores the intricacies and challenges of Vibrio-related diseases, including accurate and cost-effective diagnosis and effective control. The global burden due to emerging Vibrio species further complicates management strategies. We propose an innovative integrated technology model that harnesses cutting-edge technologies to address these obstacles. The proposed model incorporates advanced tools, such as biosensing technologies, the Internet of Things (IoT), remote sensing devices, cloud computing, and machine learning. This model offers invaluable insights and supports better decision-making by integrating real-time ecological data and biological phenotype signatures. A major advantage of our approach lies in leveraging cloud-based analytics programs, efficiently extracting meaningful information from vast and complex datasets. Collaborating with data and clinical professionals ensures logical and customized solutions tailored to each unique situation. Aquaculture biotechnology that prioritizes sustainability may have a large impact on human health and the seafood industry. Our review underscores the importance of adopting this model, revolutionizing the prognosis and management of Vibrio-related infections, even under complex circumstances. Furthermore, this model has promising implications for aquaculture and public health, addressing the United Nations Sustainable Development Goals and their development agenda.

Transcriptomic Analysis of the Liver and Brain in Grass Carp (Ctenopharyngodon idella) Under Heat Stress

Temperature is a major environmental factor that influences growth, development, metabolism, and physiological performance in fish. Grass carp (Ctenopharyngodon idella) is a highly productive fish in freshwater culture. To understand the molecular mechanism of grass carp under heat stress, we used RNA-Seq to analyze the liver and brain transcriptome of 12 libraries constructed from high-temperature (36 °C) and control (28 °C) groups. We obtained 42.49 and 42.57 GB of clean data from six liver and six brain libraries, respectively, and identified 2,534 genes that were differentially expressed in liver tissue and 1622 in brain tissue (P < 0.05). According to KEGG analysis, significant differences occurred in the expression of genes involved in metabolic and immune pathways, such as the cAMP signaling pathway, apoptosis, calcium signaling pathway, lipid metabolism, and protein processing in endoplasmic reticulum and peroxisome proliferator-activated receptor signaling pathways. This study revealed that high temperature enhanced lipid metabolism, reduced fatty acid synthesis, and disrupted the immune system of grass carp. These results investigated the molecular regulation of heat stress in grass carp and provided valuable information for the healthy culture of grass carp under high temperatures.

Effects of rrm1 on NNV Resistance Revealed by RNA-seq and Gene Editing

Viral nervous necrosis (VNN) disease caused by the nervous necrosis virus (NNV) is a major disease, leading to a huge economic loss in aquaculture. Previous GWAS and QTL mapping have identified a major QTL for NNV resistance in linkage group 20 in Asian seabass. However, no causative gene for NNV resistance has been identified. In this study, RNA-seq from brains of Asian seabass fingerlings challenged with NNV at four time points (5, 10, 15 and 20 days post-challenge) identified 1228, 245, 189 and 134 DEGs, respectively. Eight DEGs, including rrm1, were located in the major QTL for NNV resistance. An association study in 445 survived and 608 dead fingerlings after NNV challenge revealed that the SNP in rrm1 were significantly associated with NNV resistance. Therefore, rrm1 was selected for functional analysis, as a candidate gene for NNV resistance. The expression of rrm1 was significantly increased in the gill, liver, spleen and muscle, and was suppressed in the brain, gut and skin after NNV challenge. The rrm1 protein was localized in the nuclear membrane. Over-expression of rrm1 significantly decreased viral RNA and titer in NNV-infected Asian seabass cells, whereas knock-down of rrm1 significantly increased viral RNA and titer in NNV-infected Asian seabass cells. The rrm1 knockout heterozygous zebrafish was more susceptible to NNV infection. Our study suggests that rrm1 is one of the causative genes for NNV resistance and the SNP in the gene may be applied for accelerating genetic improvement for NNV resistance.

Pomc Plays an Important Role in Sexual Size Dimorphism in Tilapia

Sexual dimorphism is common across the animal kingdom. Knowledge of the mechanisms of sexual size dimorphism is limited although it is important in biology and aquaculture. Tilapia is the common name for ~ 100 species of cichlid fish. Some are important aquaculture species and males outgrow females. To gain novel insights into the mechanisms underlying sexual size dimorphism, we analyzed the differences of brain transcriptomes between males and females in Mozambique tilapia and studied the function of the pro-opiomelanocortin (Pomc) gene in tilapia and zebrafish. The transcriptome analysis identified 123, 55, and 2706 sex-biased genes at 5, 30, and 90 dph (days post-hatch), respectively, indicating sexual dimorphism of gene expressions in the brain. The expression of Pomc in the tilapia brain was a female-biased at 30, 90, and 120 dph. An analysis of the DNA sequence located upstream of the tilapia Pomc transcriptional start site identified two estrogenic response elements. In vitro luciferase assay of the two elements revealed that β-estradiol significantly enhanced the expression of luciferase activity, suggesting that the expression of Pomc is mediated by estrogen. We knocked out Pomc in zebrafish using Crispr/Cas-9. The Pomc-knockout zebrafish showed faster growth and higher sensitivity to feeding as compared to the wild-type fish. Taken together, our results indicate that Pomc contributes to sexual size dimorphism and suggest that the high estrogen level in females promotes the expression of Pomc and suppresses feeding in female tilapias, which leads to the slower growth of female tilapias.

Overview of the betta fish genome regarding species radiation, parental care, behavioral aggression, and pigmentation model relevant to humans

BACKGROUND

The Siamese fighting fish (Betta splendens, also known as the betta) is well known in aquarium markets, and also presents an exciting new research model for studying parental care, aggressive behavior, and cryptically diverse pigmentation. However, concentrated efforts are required, both in the context of conservation biology and in its genetics, to address the problems of ongoing outbreeding depression, loss of biodiversity, and lack of scientific biological information.

OBJECTIVE

The evolutionary dynamics of the betta must be better understood at the genomic scale in order to resolve the phylogenetic status of unrecognized species, develop molecular markers to study variation in traits, and identify interesting sets of genes encoding various bioresource functions.

METHODS

The recent revolution in multi-omics approaches such as genomics, transcriptomics, epigenomics, and proteomics has uncovered genetic diversity and gained insights into many aspects of betta bioresources.

RESULTS

Here, we present current research and future plans in an ongoing megaproject to characterize the betta genome as de novo assemblies, genes and repeat annotations, generating data to study diverse biological phenomena. We highlight key questions that require answers and propose new directions and recommendations to develop bioresource management to protect and enhance the betta genus.

CONCLUSION

Successful accomplishment of these plans will allow the creation of a reference annotated genome and provide valuable information at the molecular level that can be utilized to sustain biodiversity and eco-management of the betta to improve breeding programs for future biomedical research.

Twelve quick steps for genome assembly and annotation in the classroom

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.

The HIF1αn gene and its association with hypoxia tolerance in the Asian seabass

Hypoxia is one of the major challenges in aquaculture industry. Breeding of fish tolerant to hypoxia is an important task in genetic improvement of aquaculture species. The Asian seabass, Lates calcarifer, is an important foodfish species. We identified and characterized the hypoxia-inducible factor inhibitor (HIF1αn) gene in the Asian seabass. The full-length cDNA sequence of the HIF1αn was 3425 bp, with an ORF of 1065 bp, encoding 354 amino acids. The genomic sequence of the gene was 8667 bp in length, and contained eight exons and seven introns. Phylogenetic analysis of the gene in fish and tetrapods revealed that the HIF1αn in the Asian seabass was closely related to that of tilapia (Oreochromis niloticus). The HIF1αn was highly up-regulated in the gill, spleen and heart after 3.5-hours hypoxia treatment. We identified three SNPs in the third and fourth introns of the HIF1αn gene. The SNP (i.e. SNP 9332241 (C/T)) in the fourth intron was significantly (P < 0.01) associated with hypoxia tolerance. This SNP might be useful in selecting Asian seabass for improved tolerance to hypoxia. Our data also provide useful information for further detailed analysis of the function of the HIF1αn gene in hypoxia tolerance.

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Simple Summary

The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus.

Abstract

The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.

Population structure, demographic history and local adaptation of the grass carp

BACKGROUND

Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture.

RESULTS

We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow.

CONCLUSIONS

This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.