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Fish Genomics and Developmental Biology

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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: 15 May 2024 | Viewed by 10657

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Dr. Elena Sarropoulou

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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

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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 Issue Information

Dear Colleagues,

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 also involves 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

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Keywords

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

Published Papers (9 papers)

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Research

12 pages, 1588 KiB

Open AccessArticle

Genetic Structure and Diversity of Hatchery and Wild Populations of Yellow Catfish Tachysurus fulvidraco (Siluriformes: Bagridae) from Korea

by Kang-Rae Kim, Keun-Yong Kim and Ha Yoon Song

Int. J. Mol. Sci. 2024, 25(7), 3923; https://doi.org/10.3390/ijms25073923 - 31 Mar 2024

Viewed by 588

Abstract

Yellow catfish Tachysurus fulvidraco is an important commercial fish species in South Korea. However, due to their current declines in its distribution area and population size, it is being released from hatchery populations into wild populations. Hatchery populations also produced from wild broodstocks are used for its captive breeding. We reported 15 new microsatellite DNA markers of T. fulvidraco to identify the genetic diversity and structure of its hatchery and wild populations, providing baseline data for useful resource development strategies. The observed heterozygosity of the hatchery populations ranged from 0.816 to 0.873, and that of the wild populations ranged from 0.771 to 0.840. Their inbreeding coefficient ranged from −0.078 to 0.024. All populations experienced a bottleneck (p < 0.05), with effective population sizes ranging from 21 to infinity. Their gene structure was divided into two groups with STRUCTURE results of K = 2. It was confirmed that each hatchery population originated from a different wild population. This study provides genetic information necessary for the future development and conservation of fishery resources for T. fulvidraco. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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21 pages, 23740 KiB

Open AccessArticle

Exploring the Integrated Role of miRNAs and lncRNAs in Regulating the Transcriptional Response to Amino Acids and Insulin-like Growth Factor 1 in Gilthead Sea Bream (Sparus aurata) Myoblasts

by Isabel García-Pérez, Bruno Oliveira Silva Duran, Maeli Dal-Pai-Silva and Daniel Garcia de la serrana

Int. J. Mol. Sci. 2024, 25(7), 3894; https://doi.org/10.3390/ijms25073894 - 31 Mar 2024

Viewed by 601

Abstract

In this study, gilthead sea bream (Sparus aurata) fast muscle myoblasts were stimulated with two pro-growth treatments, amino acids (AA) and insulin-like growth factor 1 (Igf-1), to analyze the transcriptional response of mRNAs, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and to explore their possible regulatory network using bioinformatic approaches. AA had a higher impact on transcription (1795 mRNAs changed) compared to Igf-1 (385 mRNAs changed). Both treatments stimulated the transcription of mRNAs related to muscle differentiation (GO:0042692) and sarcomere (GO:0030017), while AA strongly stimulated DNA replication and cell division (GO:0007049). Both pro-growth treatments altered the transcription of over 100 miRNAs, including muscle-specific miRNAs (myomiRs), such as miR-133a/b, miR-206, miR-499, miR-1, and miR-27a. Among 111 detected lncRNAs (>1 FPKM), only 30 were significantly changed by AA and 11 by Igf-1. Eight lncRNAs exhibited strong negative correlations with several mRNAs, suggesting a possible regulation, while 30 lncRNAs showed strong correlations and interactions with several miRNAs, suggesting a role as sponges. This work is the first step in the identification of the ncRNAs network controlling muscle development and growth in gilthead sea bream, pointing out potential regulatory mechanisms in response to pro-growth signals. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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17 pages, 5196 KiB

Open AccessArticle

Theoretical Analysis and Expression Profiling of 17β-Hydroxysteroid Dehydrogenase Genes in Gonadal Development and Steroidogenesis of Leopard Coral Grouper (Plectropomus leopardus)

by Mingjian Liu, Hui Ding, Chaofan Jin, Mingyi Wang, Peiyu Li, Zhenmin Bao, Bo Wang and Jingjie Hu

Int. J. Mol. Sci. 2024, 25(4), 2180; https://doi.org/10.3390/ijms25042180 - 11 Feb 2024

Viewed by 876

Abstract

The differentiation and developmental trajectory of fish gonads, significantly important for fish breeding, culture, and production, has long been a focal point in the fields of fish genetics and developmental biology. However, the mechanism of gonadal differentiation in leopard coral grouper (Plectropomus leopardus) remains unclear. This study investigates the 17β-Hydroxysteroid Dehydrogenase (Hsd17b) gene family in P. leopardus, with a focus on gene characterization, expression profiling, and functional analysis. The results reveal that the P. leopardus’s Hsd17b gene family comprises 11 members, all belonging to the SDR superfamily. The amino acid similarity is only 12.96%, but conserved motifs, such as TGxxxGxG and S-Y-K, are present in these genes. Hsd17b12a and Hsd17b12b are unique homologs in fish, and chromosomal localization has confirmed that they are not derived from different transcripts of the same gene, but rather are two independent genes. The Hsd17b family genes, predominantly expressed in the liver, heart, gills, kidneys, and gonads, are involved in synthesizing or metabolizing sex steroid hormones and neurotransmitters, with their expression patterns during gonadal development categorized into three distinct categories. Notably, Hsd17b4 and Hsd17b12a were highly expressed in the testis and ovary, respectively, suggesting their involvement in the development of reproductive cells in these organs. Fluorescence in situ hybridization (FISH) further indicated specific expression sites for these genes, with Hsd17b4 primarily expressed in germ stem cells and Hsd17b12a in oocytes. This comprehensive study provides foundational insights into the role of the Hsd17b gene family in gonadal development and steroidogenesis in P. leopardus, contributing to the broader understanding of fish reproductive biology and aquaculture breeding. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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22 pages, 3628 KiB

Open AccessArticle

The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch (Sander lucioperca)

by Marieke Verleih, Tina Visnovska, Julien A. Nguinkal, Alexander Rebl, Tom Goldammer and Rune Andreassen

Int. J. Mol. Sci. 2024, 25(1), 189; https://doi.org/10.3390/ijms25010189 - 22 Dec 2023

Viewed by 599

Abstract

Micro RNAs (miRNAs) are short non-coding RNAs that act as post-transcriptional gene expression regulators. Genes regulated in vertebrates include those affecting growth and development or stress and immune response. Pikeperch (Sander lucioperca) is a species that is increasingly being considered for farming in recirculation aquaculture systems. We characterized the pikeperch miRNA repertoire to increase the knowledge of the genomic mechanisms affecting performance and health traits by applying small RNA sequencing to different developmental stages and organs. There were 234 conserved and 8 novel miRNA genes belonging to 104 families. A total of 375 unique mature miRNAs were processed from these genes. Many mature miRNAs showed high relative abundances or were significantly more expressed at early developmental stages, like the miR-10 and miR-430 family, let-7, the miRNA clusters 106-25-93, and 17-19-92. Several miRNAs associated with immune responses (e.g., slu-mir-731-5p, slu-mir-2188-5p, and slu-mir-8159-5p) were enriched in the spleen. The mature miRNAs slu-mir-203a-3p and slu-mir-205-5p were enriched in gills. These miRNAs are similarly abundant in many vertebrates, indicating that they have shared regulatory functions. There was also a significantly increased expression of the disease-associated miR-462/miR-731 cluster in response to hypoxia stress. This first pikeperch miRNAome reference resource paves the way for future functional studies to identify miRNA-associated variations that can be utilized in marker-assisted breeding programs. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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18 pages, 2368 KiB

Open AccessArticle

Exploring the Effects of Rearing Densities on Epigenetic Modifications in the Zebrafish Gonads

by Alejandro Valdivieso, Marta Caballero-Huertas, Javier Moraleda-Prados, Francesc Piferrer and Laia Ribas

Int. J. Mol. Sci. 2023, 24(21), 16002; https://doi.org/10.3390/ijms242116002 - 06 Nov 2023

Viewed by 1342

Abstract

Rearing density directly impacts fish welfare, which, in turn, affects productivity in aquaculture. Previous studies have indicated that high-density rearing during sexual development in fish can induce stress, resulting in a tendency towards male-biased sex ratios in the populations. In recent years, research has defined the relevance of the interactions between the environment and epigenetics playing a key role in the final phenotype. However, the underlying epigenetic mechanisms of individuals exposed to confinement remain elucidated. By using zebrafish (Danio rerio), the DNA methylation promotor region and the gene expression patterns of six genes, namely dnmt1, cyp19a1a, dmrt1, cyp11c1, hsd17b1, and hsd11b2, involved in the DNA maintenance methylation, reproduction, and stress were assessed. Zebrafish larvae were subjected to two high-density conditions (9 and 66 fish/L) during two periods of overlapping sex differentiation of this species (7 to 18 and 18 to 45 days post-fertilization, dpf). Results showed a significant masculinization in the populations of fish subjected to high densities from 18 to 45 dpf. In adulthood, the dnmt1 gene was differentially hypomethylated in ovaries and its expression was significantly downregulated in the testes of fish exposed to high-density. Further, the cyp19a1a gene showed downregulation of gene expression in the ovaries of fish subjected to elevated density, as previously observed in other studies. We proposed dnmt1 as a potential testicular epimarker and the expression of ovarian cyp19a1a as a potential biomarker for predicting stress originated from high densities during the early stages of development. These findings highlight the importance of rearing densities by long-lasting effects in adulthood conveying cautions for stocking protocols in fish hatcheries. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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14 pages, 11927 KiB

Open AccessArticle

Vascular Endothelial Growth Factor A (VEGFA) Regulates Hepatic Lipid and Glycogen Metabolism in Schizothorax prenanti

by Yan Wang, Jiahui Ni, Aiyu Wang, Run Zhang and Linjie Wang

Int. J. Mol. Sci. 2023, 24(20), 15171; https://doi.org/10.3390/ijms242015171 - 14 Oct 2023

Viewed by 884

Abstract

Vascular endothelial growth factor A (VEGFA) plays important roles in angiogenesis, inflammatory response as well as energy metabolism in mammals. However, its effect on glycolipid metabolism in fish has not been reported. In this study, we cloned and characterized the vegfa gene of Schizothorax prenanti (S. prenanti). vegfa expression was significantly higher in liver and muscle than that in other tissues. Then, the VEGFA recombinant protein was expressed in Escherichia coli and obtained after purification. VEGFA i.p. injection significantly increased the serum glucose and TG content compared with the control group. Moreover, VEGFA protein aggravated the glycogen and lipid deposition in the liver of S. prenanti. In addition, we found that VEGFA treatment increased hepatocyte glycogen and lipid droplet content and increased the levels of pAMPKα (T172). Furthermore, AMPKα inhibition attenuated the ability of VEGFA to induce TG and glycogen accumulation. These results demonstrate that VEGFA regulates hepatic lipid and glycogen metabolism through AMPKα in S. prenanti, which may contribute to a better understanding of VEGFA functions in the glycolipid metabolism of fish. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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20 pages, 3317 KiB

Open AccessArticle

Effects of Different Sources of Culture Substrate on the Growth and Immune Performance of the Red Swamp Crayfish (Procambarus clarkii)

by Rong Wan, Chengfeng Zhang, Yongkai Tang, Jian Zhu, Nan Yang and Shengyan Su

Int. J. Mol. Sci. 2023, 24(18), 14098; https://doi.org/10.3390/ijms241814098 - 14 Sep 2023

Viewed by 861

Abstract

The substrate in the aquatic environment plays a crucial role in nutrient deposition and recovery for the growth of aquatic organisms. In order to optimize the culture medium of Procambarus Clarkii, culture media from different sources were selected in this study to explore their effects on the growth and immune performance of red swamp crayfish. The results showed that the weight gain rate (WGR), body length growth rate (BLGR) and specific growth rate (SGR) in group I2 were the highest, followed by group I1 and group I3. The WGR and SGR of crayfish in the I1 and I2 groups were significantly higher than those in the I3 group (p < 0.05). The activities of acid phosphatase (ACP), alkaline phosphatase (AKP) and superoxide dismutase (SOD) were the highest in group I2, followed by group I3, and the lowest in group I1. The expression trends in growth-related genes, nuclear hormone receptor (E75), molt-inhibiting hormone (MIH) and chitinase genes were similar, and the expression levels in the I2 group were higher than those in the I1 and I3 groups. It was noted that the expression levels of E75 and MIH genes in the I2 group were significantly higher than those in the I3 group (p < 0.05). α diversity analysis of 16S rRNA data showed that there was no statistically significant difference in the abundance of intestinal flora among the three culture substrate groups. The β diversity in the Xitangni group, crayfish Tangni group and Shuitangni group was significantly different. These changes in microbiota suggest that using different substrates to culture crayfish leads to differences in gut microbiota diversity. To sum up, the growth in crayfish and immune performance influenced by the culture substrate condition and aquatic breeding sediment substrates, rather than crab pool and paddy field pond sediment substrates, showed a better effect. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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15 pages, 3833 KiB

Open AccessArticle

Transcriptomic Modulation Reveals the Specific Cellular Response in Chinese Sea Bass (Lateolabrax maculatus) Gills under Salinity Change and Alkalinity Stress

by Qing Zhu, Moli Li, Wei Lu, Yapeng Wang, Xujian Li and Jie Cheng

Int. J. Mol. Sci. 2023, 24(6), 5877; https://doi.org/10.3390/ijms24065877 - 20 Mar 2023

Cited by 5 | Viewed by 1602

Abstract

Salinity and alkalinity are among the important factors affecting the distribution, survival, growth and physiology of aquatic animals. Chinese sea bass (Lateolabrax maculatus) is an important aquaculture fish species in China that can widely adapt to diverse salinities from freshwater (FW) to seawater (SW) but moderately adapt to highly alkaline water (AW). In this study, juvenile L. maculatus were exposed to salinity change (SW to FW) and alkalinity stress (FW to AW). Coordinated transcriptomic responses in L. maculatus gills were investigated and based on the weighted gene co-expression network analysis (WGCNA), 8 and 11 stress-responsive modules (SRMs) were identified for salinity change and alkalinity stress, respectively, which revealed a cascade of cellular responses to oxidative and osmotic stress in L. maculatus gills. Specifically, four upregulated SRMs were enriched with induced differentially expressed genes (DEGs) for alkalinity stress, mainly corresponding to the functions of “extracellular matrix” and “anatomical structure”, indicating a strong cellular response to alkaline water. Both “antioxidative activity” and “immune response” functions were enriched in the downregulated alkaline SRMs, which comprised inhibited alkaline specific DEGs, revealing the severely disrupted immune and antioxidative functions under alkalinity stress. These alkaline-specific responses were not revealed in the salinity change groups with only moderately inhibited osmoregulation and induced antioxidative response in L. maculatus gills. Therefore, the results revealed the diverse and correlated regulation of the cellular process and stress response in saline-alkaline water, which may have arisen through the functional divergence and adaptive recruitment of the co-expression genes and will provide vital insights for the development of L. maculatus cultivation in alkaline water. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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20 pages, 5960 KiB

Open AccessArticle

Morphological and Molecular Functional Evidence of the Pharyngeal Sac in the Digestive Tract of Silver Pomfret, Pampus argenteus

by Huan Jiang, Jiabao Hu, Huihui Xie, Man Zhang, Chunyang Guo, Youyi Zhang, Yaya Li, Cheng Zhang, Shanliang Xu, Danli Wang, Xiaojun Yan, Yajun Wang and Xubo Wang

Int. J. Mol. Sci. 2023, 24(2), 1663; https://doi.org/10.3390/ijms24021663 - 14 Jan 2023

Cited by 1 | Viewed by 1794

Abstract

The pharyngeal sac is a comparatively rare organ in the digestive tract among teleost fishes. However, our understanding of this remarkable organ in the silver pomfret (Pampus argenteus) is limited. In the present study, we examined the various morphological and histological characteristics of the pharyngeal sac using histochemical techniques and electron microscopy. The pharyngeal sac showed unique characteristics such as well-developed muscular walls, weakly keratinized epithelium, numerous goblet cells, and needle-like processes on the papillae. The porous cavity of the papillae contained numerous adipocytes and was tightly enveloped by type I collagen fibers. These structures might provide mechanical protection and excellent biomechanical properties for grinding and shredding prey. A comparison of gene expression levels between the pharyngeal sac and esophagus using RNA-seq showed that phenotype-associated genes (epithelial genes and muscle genes) were upregulated, whereas genes related to nutrient digestion and absorption were downregulated in the pharyngeal sac. These results support the role of the pharyngeal sac in shredding and predigesting food. Overall, these findings provide a clearer understanding of the pharyngeal sac morphology and explain the morphological adaptations of the digestive tract for feeding on gelatinous prey. To our knowledge, this is the first report on pharyngeal sac gene expression in P. argenteus. Full article

(This article belongs to the Special Issue Fish Genomics and Developmental Biology)

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