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Fish Genomics and Developmental Biology, 2nd Edition
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Fish Genomics and Developmental Biology, 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 3374

Special Issue Editors

Dr. Elena Sarropoulou

E-Mail Website
Guest Editor
Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003 Crete, Greece
Interests: epigenetics; development; teleost; regulation; sncRNA; lncRNA; methylation; histone modification
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jorge Fernandes

E-Mail Website
Guest Editor
Faculty of Biosciences and Aquaculture, Nord University, Universitetsalleen 11, P.O. Box 1490, 8049 Bodø, Norway
Interests: genomics; development; teleost; aquaculture; transcriptomics; gene expression; environment; genomes; comparative genomics; population genomics; selective breeding; biomarker
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue on “Fish Genomics and Developmental Biology” (https://www.mdpi.com/journal/ijms/special_issues/0BZE9ZAIV6).

Genomics has had a fast scientific, social, and economic impact and is along with the rapidly advancing technologies in the spotlight of many diverse research fields. Even though the -omics area is a comparatively young branch of science, the implementation of -omics data has become a common lab practice. One of the major milestones has certainly been the invention of next-generation sequencing technologies which enabled the fast with a relatively low-cost assessment and comparison of transcriptomes and genomes. Nevertheless, the generation of large datasets involves also the challenges of accurate data processing, storage, analysis, and most importantly interpretation.

The interest in teleosts species and the model fish zebrafish (Danio rerio) in particular, first arose due to its suitability to study human-related research topics as well as to investigate early development at the molecular level. The interest in non-model teleost studies is mainly due to their economic importance in fisheries and aquaculture. Today the genomes and transcriptomes of numerous teleosts have been sequenced and are stored in publicly accessible databases. These achievements have paved the way to investigate more cross-species gene function and regulation, and to better understand the molecular bases of important mechanisms in fish biology.

The objective of the present Special Issue is to highlight the most recent genomic advances in fish biology with an emphasis on development, since numerous events and parameters have to be in congruence during embryonic and larval development to ensure well-being and health at later life stages.

Dr. Elena Sarropoulou
Prof. Dr. Jorge Fernandes
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • development
  • teleost
  • gene regulation
  • comparative genomics
  • genomics
  • aquaculture
  • transcriptomics
  • gene expression
  • environment
  • genomes
  • population genomics
  • selective breeding
  • biomarker

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Related Special Issue

Published Papers (4 papers)

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Research

18 pages, 11093 KiB  
Article
CRISPR/Cas9-Mediated Disruption of lrp6a Leads to Abnormal Median Fin Development and Somitogenesis in Goldfish (Carassius auratus)
by Huijuan Li, Rong Zhang, Xiaowen Wang, Lili Liu, Zhigang Yao and Hua Zhu
Int. J. Mol. Sci. 2025, 26(15), 7067; https://doi.org/10.3390/ijms26157067 - 22 Jul 2025
Viewed by 249
Abstract
In this study, we demonstrated that lrp6a, a co-receptor in the Wnt signaling pathway, is essential for proper median fin formation and somitogenesis in goldfish. We analyzed the gene’s sequence features and expression patterns in both wen-type and egg-type goldfish, uncovering distinct [...] Read more.
In this study, we demonstrated that lrp6a, a co-receptor in the Wnt signaling pathway, is essential for proper median fin formation and somitogenesis in goldfish. We analyzed the gene’s sequence features and expression patterns in both wen-type and egg-type goldfish, uncovering distinct tissue-specific expression differences between the two varieties. To explore the functional role of lrp6a, we performed CRISPR/Cas9-mediated gene knockout using eight designed single-guide RNAs (sgRNAs), of which four showed effective targeting. Three high-efficiency sgRNAs were selected and co-injected into embryos to achieve complete gene disruption. Morphological assessments and X-ray microtomography (μCT) imaging of the resulting mutants revealed various abnormalities, including defects in the dorsal, caudal, and anal fins, as well as skeletal deformities near the caudal peduncle. These results confirm that lrp6a plays a key role in median fin development and axial patterning, offering new insights into the genetic regulation of fin formation in teleost fish. Full article
(This article belongs to the Special Issue Fish Genomics and Developmental Biology, 2nd Edition)
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18 pages, 2791 KiB  
Article
Cortisol-Induced Chromatin Remodeling and Gene Expression in Skeletal Muscle of Rainbow Trout: Integrative ATAC-Seq and RNA-Seq Analysis
by Rodrigo Zuloaga, Camila Garrido, Luciano Ahumada-Langer, José Luis Galaz, Giorgia Daniela Ugarte, Alfredo Molina and Juan Antonio Valdés
Int. J. Mol. Sci. 2025, 26(13), 6079; https://doi.org/10.3390/ijms26136079 - 25 Jun 2025
Viewed by 502
Abstract
Cortisol, the main glucocorticoid in teleost, plays a central role in mediating the physiological response to stress by regulating metabolism, immune function, and growth. While its transcriptional effects are well known, its role in modulating chromatin accessibility in fish skeletal muscle remains poorly [...] Read more.
Cortisol, the main glucocorticoid in teleost, plays a central role in mediating the physiological response to stress by regulating metabolism, immune function, and growth. While its transcriptional effects are well known, its role in modulating chromatin accessibility in fish skeletal muscle remains poorly understood. In this study, we investigated the epigenomic and transcriptomic changes induced by cortisol in a juvenile rainbow trout’s (Oncorhynchus mykiss) skeletal muscle using ATAC-seq and RNA-seq. Fish were treated with a single intraperitoneal dose of cortisol (10 mg/kg) or vehicle, and muscle samples were collected 3 h post-treatment. ATAC-seq analysis revealed a total of 163,802 differentially accessible regions (DARs), with an important enrichment of open regions near transcription start sites and promoters. A total of 1612 and 1746 differentially accessible genes (DAGs) were identified in the cortisol and control groups, respectively. Motif enrichment analysis identified 89 transcription factors to be significantly enriched, among which key stress-responsive regulators such as Fos, AP-1, FoxO1/3, Mef2a/b/c, Klf5/10, and ATF4 were prominently represented. RNA-seq analysis identified 4050 differentially expressed genes (DEGs), with 2204 upregulated genes involved in autophagy, mitophagy, and FoxO signaling, while 1864 downregulated genes were enriched in spliceosome and chromatin remodeling pathways. Integrative analysis revealed 174 overlapping genes between ATAC-seq and RNA-seq datasets, highlighting pathways linked to autophagy and ATP-dependent chromatin remodeling. Four selected DEGs (sesn1, sesn2, cullin3, samtor) were validated by qPCR, showing high concordance with transcriptomic data. These findings provide new insights into cortisol-mediated regulation of chromatin dynamics and gene expression in teleost skeletal muscle and underscore the importance of epigenetic mechanisms in fish stress responses. Full article
(This article belongs to the Special Issue Fish Genomics and Developmental Biology, 2nd Edition)
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Graphical abstract

13 pages, 808 KiB  
Communication
Toll-like Receptor Type 2 and 13 Gene Expression and Immune Cell Profiles in Diploid and Triploid Sterlets (Acipenser ruthenus): Insights into Immune Competence in Polyploid Fish
by Olga Jablonska, Sara Duda, Szczepan Gajowniczek, Anna Nitkiewicz and Dorota Fopp-Bayat
Int. J. Mol. Sci. 2025, 26(9), 3986; https://doi.org/10.3390/ijms26093986 - 23 Apr 2025
Viewed by 521
Abstract
Toll-like receptors (TLRs) are key components of the innate immune system in fish, responsible for recognizing pathogen-associated molecular patterns derived from bacteria, viruses, and fungi. The sterlet (Acipenser ruthenus), an endangered sturgeon species valued for its meat and caviar, is a [...] Read more.
Toll-like receptors (TLRs) are key components of the innate immune system in fish, responsible for recognizing pathogen-associated molecular patterns derived from bacteria, viruses, and fungi. The sterlet (Acipenser ruthenus), an endangered sturgeon species valued for its meat and caviar, is a promising model for studying the effects of polyploidy on immune gene regulation. This study examined the expression of Toll-like receptor type 2 (TLR2) and type 13 (TLR13) in the heart, liver, gills, spleen, and kidney of diploid and triploid healthy sterlets using real-time PCR. TLR2 and TLR13 were expressed in all tissues of both diploids and triploids. In diploids, TLR2 expression was the highest in the kidney and the lowest in the liver (p < 0.05). Similarly, TLR13 expression in diploids was highest in the kidney and gills, and lowest in the liver (p < 0.05). In triploids, no significant tissue-specific variation in TLR expression was observed (p > 0.05). Comparisons between diploid and triploid sterlets revealed higher TLR2 expression in the kidney and higher TLR13 expression in the heart and kidney of diploids (p < 0.05). These molecular findings were supported by leukocyte analysis, which showed a significantly lower percentage of lymphocytes and a higher proportion of neutrophils in triploids compared to diploids. Additionally, the proportion of thrombocytes was significantly elevated in triploids (p < 0.05). This study provides the first report of TLR expression in polyploid fish, offering new insights into immune modulation associated with polyploidy in sturgeons. Full article
(This article belongs to the Special Issue Fish Genomics and Developmental Biology, 2nd Edition)
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12 pages, 2876 KiB  
Article
Genome-Wide Association Study of Resistance to Largemouth Bass Ranavirus (LMBV) in Micropterus salmoides
by Pinhong Li, Xia Luo, Shaozhi Zuo, Xiaozhe Fu, Qiang Lin, Yinjie Niu, Hongru Liang, Baofu Ma and Ningqiu Li
Int. J. Mol. Sci. 2024, 25(18), 10036; https://doi.org/10.3390/ijms251810036 - 18 Sep 2024
Cited by 3 | Viewed by 1502
Abstract
The disease caused by Largemouth bass ranavirus (LMBV) is one of the most severe viral diseases in largemouth bass (Micropterus salmoides). It is crucial to evaluate the genetic resistance of largemouth bass to LMBV and develop markers for disease-resistance breeding. In [...] Read more.
The disease caused by Largemouth bass ranavirus (LMBV) is one of the most severe viral diseases in largemouth bass (Micropterus salmoides). It is crucial to evaluate the genetic resistance of largemouth bass to LMBV and develop markers for disease-resistance breeding. In this study, 100 individuals (45 resistant and 55 susceptible) were sequenced and evaluated for resistance to LMBV and a total of 2,579,770 variant sites (SNPs-single-nucleotide polymorphisms (SNPs) and insertions–deletions (InDels)) were identified. A total of 2348 SNPs-InDels and 1018 putative candidate genes associated with LMBV resistance were identified by genome-wide association analyses (GWAS). Furthermore, GO and KEGG analyses revealed that the 10 candidate genes (MHC II, p38 MAPK, AMPK, SGK1, FOXO3, FOXO6, S1PR1, IL7R, RBL2, and GADD45) were related to intestinal immune network for IgA production pathway and FoxO signaling pathway. The acquisition of candidate genes related to resistance will help to explore the molecular mechanism of resistance to LMBV in largemouth bass. The potential polymorphic markers identified in this study are important molecular markers for disease resistance breeding in largemouth bass. Full article
(This article belongs to the Special Issue Fish Genomics and Developmental Biology, 2nd Edition)
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