Aquaculture Omics: Current Status and Future Perspectives

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

Deadline for manuscript submissions: 15 October 2026 | Viewed by 201

Editor


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Guest Editor
1. Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2. Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), 57001 Thessaloniki, Greece
Interests: omics; aquaculture; traceability; species identification; population genetics
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Special Issue Information

Dear Colleagues,

Aquaculture stands as the fastest-growing food production sector, poised to meet escalating global protein demands amid declining wild fisheries. However, challenges like disease outbreaks, environmental stressors, and genetic limitations hinder sustainable intensification. In this context, "omics" technologies—genomics, transcriptomics, proteomics, metabolomics, and epigenomics—have unlocked unprecedented insights into aquatic organism biology, enabling precision breeding, health management, and resilience enhancement.

In this Special Issue, ‘Aquaculture Omics: Current Status and Future Perspectives’, we aim to synthesize cutting-edge advancements and chart transformative pathways forward. We invite the submission of original research, reviews, and perspectives that explore omics applications across species. Key foci include genomic selection for growth and disease resistance, multi-omics integration for stress response mechanisms, microbiome dynamics in production systems, and epigenetic innovations for environmental adaptation.

Building on foundational works, this Special Issue will bridge gaps in translational research. We will highlights persistent hurdles, such as data standardization and equitable access in developing regions, while envisioning AI-driven omics for climate-resilient aquaculture. By converging global expertise, we will propel omics from bench to scalable practice, fostering a sustainable blue revolution.

Dr. Konstantinos Gkagkavouzis
Guest Editor

Manuscript Submission Information

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Keywords

  • aquaculture omics
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • epigenomics
  • sustainable aquaculture
  • disease resistance
  • genomic selection
  • climate resilience

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Published Papers (1 paper)

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Research

20 pages, 7064 KB  
Article
LncRNA-Mediated Transcriptional Responses to Piscirickettsia salmonis Infection in Rainbow Trout Skeletal Muscle and Primary Myotubes
by Rodrigo Zuloaga, Luciano Ahumada-Langer, Phillip Dettleff, Alfredo Molina and Juan Antonio Valdés
Fishes 2026, 11(7), 398; https://doi.org/10.3390/fishes11070398 (registering DOI) - 6 Jul 2026
Abstract
Piscirickettsia salmonis is one of the most significant pathogens affecting salmon farming. Besides liver, head kidney and spleen, skeletal muscle has shown transcriptional immune responses to these bacteria, but the contribution of non-coding RNAs remains poorly understood. This study investigates the role of [...] Read more.
Piscirickettsia salmonis is one of the most significant pathogens affecting salmon farming. Besides liver, head kidney and spleen, skeletal muscle has shown transcriptional immune responses to these bacteria, but the contribution of non-coding RNAs remains poorly understood. This study investigates the role of long non-coding RNAs (lncRNAs) in the immune response of rainbow trout skeletal muscle and primary myotube cultures infected with P. salmonis. Using RNA-seq data from both in vivo and in vitro muscle under control and infected conditions, the analysis identified 4263 candidate lncRNAs through a stringent bioinformatics pipeline. These lncRNAs were mostly classified as exonic and intergenic, showing distinct genomic distributions and structural differences depending on the source. Expression analyses revealed that cell type had a stronger effect on lncRNA profiles than infection status. From 764 differentially expressed lncRNAs, 191 were uniquely associated with infected and 180 with control conditions, mainly unannotated. Functional predictions based on co-expression and proximity to coding genes suggest that lncRNAs are primarily involved in downregulation of structural-cellular maintenance under control conditions, whereas during infection, they are related to immunity, signaling, and apoptosis. Overall, the findings indicate that lncRNAs exhibit origin-specific regulatory roles and are modulated by P. salmonis infection, highlighting their potential importance in fish immune responses. Full article
(This article belongs to the Special Issue Aquaculture Omics: Current Status and Future Perspectives)
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