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Aquaculture Genetics: Latest Advances and Prospects
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Aquaculture Genetics: Latest Advances and Prospects

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (10 December 2022) | Viewed by 9292

Special Issue Editors

Dr. Antonio Figueras

E-Mail Website
Guest Editor
Instituto de Investigaciones Marinas, IIM-CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
Interests: aquaculture; fish; shellfish; genetics; genomics; transcriptomic; epigenomics
Special Issues, Collections and Topics in MDPI journals
Dr. Magali Rey

E-Mail Website
Guest Editor
Instituto de Investigaciones Marinas, IIM-CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
Interests: aquaculture; invertebrates; immunology; host-pathogen interaction; transcriptome response; gene modulation; antiviral response
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Overfishing is an important concern, mainly due to the ongoing increase in the size of the human population. Fortunately, aquaculture has emerged as an alternative supply of fish and shellfish. In recent years, although capture fishery production has been remained at approximately 90 million tonnes per year, aquaculture has continued to show sustained growth, amounting to 80 million tonnes in recent years. Therefore, fish and shellfish aquacultures represent a powerful economic sector all around the world.

The lowering cost of massive sequencing technologies over recent years has enabled the genome sequencing of numerous fish and shellfish species with relevance in the aquaculture industry. This represents an important tool for geneticists, since whole-genome availability facilitates the search for genetic markers or genes associated with different traits of interest. Massive transcriptome analyses have also become indispensable to the study of different questions of interest (nutrition, growth, immune response, reproduction, etc.). More recently, the study of the epigenome is being rapidly expanded to aquaculture research.

Due to the success of the previous Special Issue “Genetic Research in Aquaculture” (https://www.mdpi.com/journal/genes/special_issues/Aquaculture_Genetic_Research), we would like to launch a second edition. This Special Issue welcomes papers in the field of the genetics and genomics of fish, shellfish and other species of interest in aquaculture, including the identification of genetic markers, gene variants, genome sequencing, and transcriptome and epigenome analyses. Manuscripts focusing on high-throughput technologies will be welcomed, although the topic covers all aspects related to genetic research in aquaculture.

Dr. Antonio Figueras
Dr. Magali Rey
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • aquaculture
  • fish
  • shellfish
  • genetics
  • genomics
  • transcriptomics
  • epigenomics
  • high-throughput technologies

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Published Papers (4 papers)

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25 pages, 7695 KiB  
Article
Unveiling the Impact of Gene Presence/Absence Variation in Driving Inter-Individual Sequence Diversity within the CRP-I Gene Family in Mytilus spp.
by Nicolò Gualandi, Davide Fracarossi, Damiano Riommi, Marco Sollitto, Samuele Greco, Mario Mardirossian, Sabrina Pacor, Tiago Hori, Alberto Pallavicini and Marco Gerdol
Genes 2023, 14(4), 787; https://doi.org/10.3390/genes14040787 - 24 Mar 2023
Cited by 1 | Viewed by 2059
Abstract
Mussels (Mytilus spp.) tolerate infections much better than other species living in the same marine coastal environment thanks to a highly efficient innate immune system, which exploits a remarkable diversification of effector molecules involved in mucosal and humoral responses. Among these, antimicrobial [...] Read more.
Mussels (Mytilus spp.) tolerate infections much better than other species living in the same marine coastal environment thanks to a highly efficient innate immune system, which exploits a remarkable diversification of effector molecules involved in mucosal and humoral responses. Among these, antimicrobial peptides (AMPs) are subjected to massive gene presence/absence variation (PAV), endowing each individual with a potentially unique repertoire of defense molecules. The unavailability of a chromosome-scale assembly has so far prevented a comprehensive evaluation of the genomic arrangement of AMP-encoding loci, preventing an accurate ascertainment of the orthology/paralogy relationships among sequence variants. Here, we characterized the CRP-I gene cluster in the blue mussel Mytilus edulis, which includes about 50 paralogous genes and pseudogenes, mostly packed in a small genomic region within chromosome 5. We further reported the occurrence of widespread PAV within this family in the Mytilus species complex and provided evidence that CRP-I peptides likely adopt a knottin fold. We functionally characterized the synthetic peptide sCRP-I H1, assessing the presence of biological activities consistent with other knottins, revealing that mussel CRP-I peptides are unlikely to act as antimicrobial agents or protease inhibitors, even though they may be used as defense molecules against infections from eukaryotic parasites. Full article
(This article belongs to the Special Issue Aquaculture Genetics: Latest Advances and Prospects)
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13 pages, 2529 KiB  
Article
Effect of 11-Deoxycorticosterone in the Transcriptomic Response to Stress in Rainbow Trout Skeletal Muscle
by Rodrigo Zuloaga, Daniela Aravena-Canales, Jorge Eduardo Aedo, Cesar Osorio-Fuentealba, Alfredo Molina and Juan Antonio Valdés
Genes 2023, 14(2), 512; https://doi.org/10.3390/genes14020512 - 17 Feb 2023
Cited by 3 | Viewed by 2146
Abstract
In aquaculture, many stressors can negatively affect growth in teleosts. It is believed that cortisol performs glucocorticoid and mineralocorticoid functions because teleosts do not synthesize aldosterone. However, recent data suggest that 11-deoxycorticosterone (DOC) released during stress events may be relevant to modulate the [...] Read more.
In aquaculture, many stressors can negatively affect growth in teleosts. It is believed that cortisol performs glucocorticoid and mineralocorticoid functions because teleosts do not synthesize aldosterone. However, recent data suggest that 11-deoxycorticosterone (DOC) released during stress events may be relevant to modulate the compensatory response. To understand how DOC modifies the skeletal muscle molecular response, we carried out a transcriptomic analysis. Rainbow trout (Oncorhynchus mykiss) were intraperitoneally treated with physiological doses of DOC in individuals pretreated with mifepristone (glucocorticoid receptor antagonist) or eplerenone (mineralocorticoid receptor antagonist). RNA was extracted from the skeletal muscles, and cDNA libraries were constructed from vehicle, DOC, mifepristone, mifepristone plus DOC, eplerenone, and eplerenone plus DOC groups. The RNA-seq analysis revealed 131 differentially expressed transcripts (DETs) induced by DOC with respect to the vehicle group, mainly associated with muscle contraction, sarcomere organization, and cell adhesion. In addition, a DOC versus mifepristone plus DOC analysis revealed 122 DETs related to muscle contraction, sarcomere organization, and skeletal muscle cell differentiation. In a DOC versus eplerenone plus DOC analysis, 133 DETs were associated with autophagosome assembly, circadian regulation of gene expression, and regulation of transcription from RNA pol II promoter. These analyses indicate that DOC has a relevant function in the stress response of skeletal muscles, whose action is differentially modulated by GR and MR and is complementary to cortisol. Full article
(This article belongs to the Special Issue Aquaculture Genetics: Latest Advances and Prospects)
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21 pages, 2471 KiB  
Article
A Transcriptomic Analysis of Phenotypic Plasticity in Crassostrea virginica Larvae under Experimental Acidification
by Michelle Barbosa, Caroline Schwaner, Emmanuelle Pales Espinosa and Bassem Allam
Genes 2022, 13(9), 1529; https://doi.org/10.3390/genes13091529 - 25 Aug 2022
Cited by 10 | Viewed by 2154
Abstract
Ocean acidification (OA) is a major threat to marine calcifiers, and little is known regarding acclimation to OA in bivalves. This study combined physiological assays with next-generation sequencing to assess the potential for recovery from and acclimation to OA in the eastern oyster [...] Read more.
Ocean acidification (OA) is a major threat to marine calcifiers, and little is known regarding acclimation to OA in bivalves. This study combined physiological assays with next-generation sequencing to assess the potential for recovery from and acclimation to OA in the eastern oyster (Crassostrea virginica) and identify molecular mechanisms associated with resilience. In a reciprocal transplant experiment, larvae transplanted from elevated pCO2 (~1400 ppm) to ambient pCO2 (~350 ppm) demonstrated significantly lower mortality and larger size post-transplant than oysters remaining under elevated pCO2 and had similar mortality compared to those remaining in ambient conditions. The recovery after transplantation to ambient conditions demonstrates the ability for larvae to rebound and suggests phenotypic plasticity and acclimation. Transcriptomic analysis supported this hypothesis as genes were differentially regulated under OA stress. Transcriptomic profiles of transplanted and non-transplanted larvae terminating in the same final pCO2 converged, further supporting the idea that acclimation underlies resilience. The functions of differentially expressed genes included cell differentiation, development, biomineralization, ion exchange, and immunity. Results suggest acclimation as a mode of resilience to OA. In addition, the identification of genes associated with resilience can serve as a valuable resource for the aquaculture industry, as these could enable marker-assisted selection of OA-resilient stocks. Full article
(This article belongs to the Special Issue Aquaculture Genetics: Latest Advances and Prospects)
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12 pages, 1727 KiB  
Brief Report
The Coding Mitogenome of the Freshwater Crayfish Pontastacus leptodactylus (Decapoda:Astacidea:Astacidae) from Lake Vegoritida, Greece and Its Taxonomic Classification
by Maria V. Alvanou, Apostolos P. Apostolidis, Athanasios Lattos, Basile Michaelidis and Ioannis A. Giantsis
Genes 2023, 14(2), 494; https://doi.org/10.3390/genes14020494 - 15 Feb 2023
Cited by 6 | Viewed by 1890
Abstract
Pontastacus leptodactylus (Eschscholtz, 1823) (Decapoda:Astacidea:Astacidae) constitutes an ecologically and economically highly important species. In the present study, the mitochondrial genome of the freshwater crayfish P. leptodactylus from Greece is analyzed for the first time, using 15 newly designed primer pairs based on available [...] Read more.
Pontastacus leptodactylus (Eschscholtz, 1823) (Decapoda:Astacidea:Astacidae) constitutes an ecologically and economically highly important species. In the present study, the mitochondrial genome of the freshwater crayfish P. leptodactylus from Greece is analyzed for the first time, using 15 newly designed primer pairs based on available sequences of closely related species. The analyzed coding part of the mitochondrial genome of P. leptodactylus consists of 15,050 base pairs including 13 protein-coding genes (PCGs), 2 ribosomal RNA gene (rRNAs), and 22 transfer RNA genes (tRNAs). These newly designed primers may be particularly useful in future studies for analyzing different mitochondrial DNA segments. Based on the entire mitochondrial genome sequence, compared to other haplotypes from related species belonging in the same family (Astacidae) available in the GenBank database, a phylogenetic tree was constructed depicting the phylogenetic relationships of P. leptodactylus. Based on the results, the genetic distance between Astacus astacus and P. leptodactylus is smaller than the genetic distance between Austropotamobius pallipes and Austropotamobius torrentium, despite the fact that the latter two are classified within the same genus, questioning the phylogenetic position of A. astacus as a different genus than P. leptodactylus. In addition, the sample from Greece seems genetically distant compared with a conspecific haplotype available in the GenBank database, possibly implying a genetic distinction of P. leptodactylus from Greece. Full article
(This article belongs to the Special Issue Aquaculture Genetics: Latest Advances and Prospects)
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