Omics in Fish Aquaculture and Fisheries

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 8632

Special Issue Editors

1. Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2. Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Buildings A & B, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece
Interests: omics; aquaculture; traceability; species identification; population genetics
1. Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2. Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Buildings A & B, Thessaloniki, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece
Interests: food traceability; species identification; NGS; population genetics
1. Department of Life Sciences, University of Trieste, Trieste, Italy
2. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Sgonico, Italy
Interests: mollusc comparative genomics; biodiversity assessment with molecular tools; DNA metabarcoding; environmental DNA; gene expression; transcriptomics; molecular immunology; marine biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Omics is a term covering modern technologies like genomics, proteomics, transcriptomics and metabolomics. Such techniques are receiving increased recognition due to their high potential to unravel novel mechanisms in biological science. NGS led in the revolution of genomics. Proteomics and transcriptomics technology provides a powerful set of tools for functional genomics studies. Metabolomics allows the measurement of low molecular weight endogenous metabolites and provides an overview of the metabolic status of a biological system. Data generated from omics can be linked together through bioinformatic analyses to generate an overall approach to events occurring within a given organism. Omics technology is being already used in the fisheries and aquaculture sector for unraveling the mechanisms of growth, disease and stress tolerance, selection of disease-resistant varieties, fish disease diagnosis, vaccine development, population structure, species identification for fish food authentication, post-harvest value addition, etc. However, there is always a challenge to apply omics to fish species, so I am pleased to invite you to contribute to the Special Issue “Omics in Fish Aquaculture and Fisheries” in the Fishes journal.

Dr. Konstantinos Gkagkavouzis
Dr. Styliani Minoudi
Prof. Dr. Alberto Pallavicini
Guest Editors

Manuscript Submission Information

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Keywords

  • omics
  • fisheries
  • aquaculture
  • fish
  • NGS

Published Papers (5 papers)

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Research

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8 pages, 3188 KiB  
Communication
Changes in the Gut Microbiota Composition of Juvenile Olive Flounder (Paralichthys olivaceus) Caused by Pathogenic Bacterial Infection
by Dong-Gyun Kim, Su-Jeong Lee, Jong Min Lee, Eun-Woo Lee and Won Je Jang
Fishes 2023, 8(6), 294; https://doi.org/10.3390/fishes8060294 - 01 Jun 2023
Cited by 1 | Viewed by 1094
Abstract
The fish gut microbiota plays an important role in overall health. However, few reports have described the changes in the composition of gut microbiota following infection with pathogenic bacteria in olive flounder (Paralichthys olivaceus). Here, we reported the changes in the [...] Read more.
The fish gut microbiota plays an important role in overall health. However, few reports have described the changes in the composition of gut microbiota following infection with pathogenic bacteria in olive flounder (Paralichthys olivaceus). Here, we reported the changes in the gut microbiota composition of flounder after treatment with each of the three pathogenic bacteria (Edwardsiella tarda, Streptococcus iniae, and Vibrio harveyi). Edwardsiella tarda infection decreased the relative abundance of Verrucomicrobia and increased Proteobacteria abundance at the phylum level of the gut microbiota over time. Similarly, Streptococcus iniae infection reduced the relative abundance of Verrucomicrobia. Vibrio harveyi infection caused a decrease in the relative abundance of Firmicutes and Verrucomicrobia and increased Proteobacteria. At the genus level, infection with all three pathogens increased the relative abundance of Ralstonia and Sphingomonas species. Conversely, this infection decreased the relative abundances of Rubritalea, Saccharimonas, and Bacillus species. Therefore, reducing the abundance of Ralstonia and Sphingomonas and increasing the abundance of Rubritalea, Saccharimonas, and Bacillus in the gut microbiota composition of flounder might help maintain a healthy gut microbiota balance. This research might be useful for future studies on improving the health of flounder through gut microbiota regulation. Full article
(This article belongs to the Special Issue Omics in Fish Aquaculture and Fisheries)
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17 pages, 2757 KiB  
Article
Untargeted Metabolomics Associated with Behavioral and Toxicological Studies Yield Insights into the Impact of 2,6-Dichloro-3-hydroxy-1,4-benzoquinone Disinfection By-Product on Zebrafish Larvae
by Ieremias Chousidis, Theodoros Chatzimitakos, Constantine Stalikas and Ioannis Leonardos
Fishes 2022, 7(6), 368; https://doi.org/10.3390/fishes7060368 - 02 Dec 2022
Cited by 1 | Viewed by 1276
Abstract
The disinfection by-product 2,6-dichloro-3-hydroxy-1,4-benzoquinone (2,6-DCBQ-OH) is a halobenzoquinone that emerges after chlorination. Therefore, it will inevitably come into contact with aquatic organisms. The aim of this study was to investigate the effect of 2,6-DCBQ-OH on zebrafish embryos. The dose-dependent toxicity was recorded, and [...] Read more.
The disinfection by-product 2,6-dichloro-3-hydroxy-1,4-benzoquinone (2,6-DCBQ-OH) is a halobenzoquinone that emerges after chlorination. Therefore, it will inevitably come into contact with aquatic organisms. The aim of this study was to investigate the effect of 2,6-DCBQ-OH on zebrafish embryos. The dose-dependent toxicity was recorded, and the LC50 value was found to be 186 μg/L. Toxicity was accompanied with morphological, developmental, and behavioral abnormalities, and metabolic alterations. The association of phenotypic alterations with metabolic alterations was investigated through metabolomic study. In the control group, 25 metabolic pathways were identified, and 10 of them remained unaffected upon exposure to the halobenzoquinone. The upregulation of the glutathione pathway suggested that 2,6-DCBQ-OH can cause oxidative stress. In addition, the upregulation of the β-alanine metabolism pathway may be associated with the observed reduced swimming activity observed. Likewise, the downregulation of pathways associated with glycerophospholipids and butyrate can result in endocrine disruption, ineffective regulation of weight and body composition, and glucose homeostasis. The fatty acid elongation and synthesis of essential amino acids are downregulated, which can be associated with insufficient organogenesis at early life stages. In conclusion, exposure of zebrafish to 2,6-DCBQ-OH results in dysregulation and metabolic collapse of the organism, which ultimately result in developmental, morphological, behavioral, and other abnormalities. Full article
(This article belongs to the Special Issue Omics in Fish Aquaculture and Fisheries)
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17 pages, 3540 KiB  
Article
RNA-Seq Analysis of the Key Long Noncoding RNAs and mRNAs Related to the Regulation of Hepatic Lipid Metabolism in Oreochromis niloticus
by Yifan Tao, Siqi Lu, Tao Zheng, Mingxiao Li, Jun Qiang and Pao Xu
Fishes 2022, 7(6), 332; https://doi.org/10.3390/fishes7060332 - 11 Nov 2022
Cited by 1 | Viewed by 1263
Abstract
Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalances and fatty liver disease during intensive farming. Long non-coding RNAs (lncRNAs) perform essential roles in various biological processes, including lipid metabolism. However, the lncRNAs involved in hepatic lipid [...] Read more.
Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalances and fatty liver disease during intensive farming. Long non-coding RNAs (lncRNAs) perform essential roles in various biological processes, including lipid metabolism. However, the lncRNAs involved in hepatic lipid metabolism in tilapia have not yet been identified. In this study, Illumina sequencing and bioinformatic analyses were performed on the liver of juvenile male GIFT fed a high-fat diet (HFD, 18.5% lipid) or a normal-fat diet (NFD, 8% lipid) for 56 days. RNA-seq analyses revealed 299 differentially expressed (DE)-mRNAs and 284 DE-lncRNAs between these two groups. The transcript profiles of 14 candidates (seven DE-mRNA and seven DE-lncRNAs) were verified by qRT-PCR, and the results were consistent with the RNA-seq results. Furthermore, 65 cis target genes and 3610 trans target genes of DE-lncRNAs were predicted. Functional analyses suggested that multiple metabolic pathways are affected by a high fat intake, including the PPAR signaling, fatty acid degradation, and fatty acid metabolism pathways. A co-expression network analysis indicated that many lncRNAs interact with numerous genes involved in lipid metabolism, and that some genes are regulated by multiple lncRNAs. The expression patterns of three lncRNAs (MSTRG.14598.1, MSTRG.6725.3, and MSTRG.13364.2) and their potential target genes (faldh, slc25a48, and fabp7a) in the PPAR signaling pathway were investigated. Our study provides new information about lncRNAs associated with lipid metabolism in tilapia. Full article
(This article belongs to the Special Issue Omics in Fish Aquaculture and Fisheries)
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14 pages, 2189 KiB  
Article
Multi-Omics Data Reveal Amino Acids Related Genes in the Common Carp Cyprinus carpio
by Hanyuan Zhang, Youxiu Zhu, Peng Xu, Zixia Zhao, Jianxin Feng, Biyin Wu, Yanliang Jiang, Chuanju Dong and Jian Xu
Fishes 2022, 7(5), 225; https://doi.org/10.3390/fishes7050225 - 29 Aug 2022
Cited by 1 | Viewed by 1803
Abstract
Amino acids have important physiological effects on fish growth and development and are essential nutrition for humans. Flavor-related amino acids, such as glutamic acid and glycine, could have a significant effect on the taste of fish flesh. However, studies on the genetic mechanisms [...] Read more.
Amino acids have important physiological effects on fish growth and development and are essential nutrition for humans. Flavor-related amino acids, such as glutamic acid and glycine, could have a significant effect on the taste of fish flesh. However, studies on the genetic mechanisms of amino acid metabolism in common carp (Cyprinus carpio) are still limited. This study identified divergent patterns on the genomic, transcriptomic and epigenomic levels in two groups of common carp with different amino acid contents. After genome-wide association analysis, a total of 62 genes was found to be associated with glycine, proline and tyrosine content. Transcriptome analysis of essential amino acids, branched-chain amino acids and flavor-related amino acids were performed using brain, liver and muscle tissues, resulting in 1643 differentially expressed genes (DEGs). Whole-genome bisulfite sequencing identified 3108 genes with differentially methylated promoters (DMPs). After the enrichment analysis, a series of pathways associated with amino acid metabolism, including growth regulation, lipid metabolism and the citrate cycle, was revealed. Integrated studies showed a strong correlation between DEGs and DMPs for amino acid contents in brain and muscle tissues. These multi-omics data revealed candidate genes and pathways related to amino acid metabolism in C. carpio. Full article
(This article belongs to the Special Issue Omics in Fish Aquaculture and Fisheries)
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Review

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22 pages, 2023 KiB  
Review
Decoding the Transcriptome of Sharks, Rays, and Chimaeras: Insights into Their Physiology, Morphology, Evolution, and Biomedical Applications
by Manuel J. Seixas, Rodrigo R. Domingues and Agostinho Antunes
Fishes 2023, 8(5), 271; https://doi.org/10.3390/fishes8050271 - 19 May 2023
Cited by 2 | Viewed by 2183
Abstract
Chondrichthyes (including sharks, rays, and chimaeras) are a class of jawed cartilaginous fishes (with skeletons composed primarily of cartilage), with major relevance to the marine ecosystems and to humanity. However, cartilaginous fishes are facing various threatens, inflicting abrupt declines in their populations. Thus, [...] Read more.
Chondrichthyes (including sharks, rays, and chimaeras) are a class of jawed cartilaginous fishes (with skeletons composed primarily of cartilage), with major relevance to the marine ecosystems and to humanity. However, cartilaginous fishes are facing various threatens, inflicting abrupt declines in their populations. Thus, critical assessment of available molecular genetic variation, particularly retrieved from Chondrichthyans’ transcriptomic analyses, represents a major resource to foster genomics research in this ancient group of vertebrate species. Briefly, RNA-Seq involves the sequencing of RNA strands present on a target tissue, which can assist genome annotation and elucidate genetic features on species without a sequenced genome. The resulting information can unravel responses of an individual to environmental changes, evolutionary processes, and support the development of biomarkers. We scrutinized more than 800 RNA-Seq entries publicly available, and reviewed more than one decade of available transcriptomic knowledge in chondrichthyans. We conclude that chondrichthyans’ transcriptomics is a subject in early development, since not all the potential of this technology has been fully explored, namely their use to prospectively preserve these endangered species. Yet, the transcriptomic database provided findings on the vertebrates’ evolution, chondrichthyans’ physiology, morphology, and their biomedical potential, a trend likely to expand further in the future. Full article
(This article belongs to the Special Issue Omics in Fish Aquaculture and Fisheries)
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