Research

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9 pages, 888 KiB

Open AccessArticle

Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis

by Sichen Zheng, Yancui Chen, Biao Wu, Liqing Zhou, Zhihong Liu, Tianshi Zhang and Xiujun Sun

Animals 2024, 14(4), 542; https://doi.org/10.3390/ani14040542 - 06 Feb 2024

Viewed by 565

Abstract

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully [...] Read more.

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of F_IS was estimated to be from −0.9643 to 1.0000. The global F_st value was 0.1248 (p < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy–Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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13 pages, 998 KiB

Open AccessFeature PaperArticle

MassArray Genotyping as a Selection Tool for Extending the Shelf-Life of Fresh Gilthead Sea Bream and European Seabass

by Rafael Angelakopoulos, Andreas Tsipourlianos, Themistoklis Giannoulis, Zissis Mamuris and Katerina A. Moutou

Animals 2024, 14(2), 205; https://doi.org/10.3390/ani14020205 - 08 Jan 2024

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Abstract

In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary [...] Read more.

In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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16 pages, 996 KiB

Open AccessArticle

Influence of Storage Time on the DNA Integrity and Viability of Spermatozoa of the Spider Crab Maja brachydactyla

by Elba Rodríguez-Pena, Diego Suárez, Graciela Estévez-Pérez, Patricia Verísimo, Noelia Barreira, Luis Fernández, Ana González-Tizón and Andrés Martínez-Lage

Animals 2023, 13(22), 3555; https://doi.org/10.3390/ani13223555 - 17 Nov 2023

Viewed by 757

Abstract

Natural populations of the spider crab Maja brachydactyla constitute a fishery resource of great economic importance in many countries. As in the rest of eubrachyurans, the females of this species have ventral-type seminal receptacles where they store sperm from copulations. Sperm can be [...] Read more.

Natural populations of the spider crab Maja brachydactyla constitute a fishery resource of great economic importance in many countries. As in the rest of eubrachyurans, the females of this species have ventral-type seminal receptacles where they store sperm from copulations. Sperm can be stored in these structures for months and even years before egg fertilisation, with the consequent degradation of the sperm cells during the time. In this work, we analyse the viability and the possible genetic damage in sperm accumulated in the seminal receptacles of M. brachydactyla females as a function of the storage time (from 0 to 14 months) using the comet assay technique. On one hand, we developed an algorithm for comet image analysis that improves the comet segmentation compared with the free software Open comet v1.3.1 (97% vs. 76% of detection). In addition, our software allows the manual modification of the contours wrongly delimited via the automatic tool. On the other hand, our data show a sharp decline in sperm viability and DNA integrity in the first four months of storage, which could lead to a decrease in the fecundity rate and/or viability of the embryos or larvae from the second and third clutches of the annual cycle if the repair capacity in these gametic cells is low. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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28 pages, 4145 KiB

Open AccessArticle

Trends of Eurasian Perch (Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene

by Adomas Ragauskas, Ieva Ignatavičienė, Vytautas Rakauskas, Dace Grauda, Petras Prakas and Dalius Butkauskas

Animals 2023, 13(19), 3057; https://doi.org/10.3390/ani13193057 - 29 Sep 2023

Cited by 1 | Viewed by 771

Abstract

The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability [...] Read more.

The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability and microevolution of Perca fluviatilis within phylogeographic and anthropogenic contexts. We sequenced a 627 bp fragment encompassing the ATP6 region and used it for genetic analysis of 193 perch caught in Latvia, Lithuania, Belarus, and Ukraine, representing natural and anthropogenically impacted populations. We evaluated patterns of intraspecific genetic diversity in the ATP6 region and phylogeographic trends within the studied area compared with previously established D-loop trends. Evaluation of ATP6 coding sequence variability revealed that among 13 newly detected haplotypes, only two were caused by non-synonymous substitutions of amino acids of the protein. PCoA revealed three genetic groups (I–III) based on the ATP6 region that encompassed four previously described genetic groups established based on the mtDNA D-loop. The two mtDNA regions (D-loop and ATP6) have microevolved at least partially independently. Prolonged anthropogenic impacts may generate new point mutations at the ATP6 locus, but this phenomenon could be mainly concealed by natural selection and reparation processes. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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19 pages, 2599 KiB

Open AccessArticle

I Like This New Me: Unravelling Population Structure of Mediterranean Electric Rays and Taxonomic Uncertainties within Torpediniformes

by Riccardo Melis, Simone Di Crescenzo, Alessia Cariani, Alice Ferrari, Valentina Crobe, Andrea Bellodi, Antonello Mulas, Laura Carugati, Elisabetta Coluccia, Maria Cristina Follesa and Rita Cannas

Animals 2023, 13(18), 2899; https://doi.org/10.3390/ani13182899 - 13 Sep 2023

Viewed by 903

Abstract

The present study focused on the three species of electric rays known to occur in the Mediterranean Sea: Torpedo torpedo, Torpedo marmorata and Tetronarce nobiliana. Correct identification of specimens is needed to properly assess the impact of fisheries on populations and [...] Read more.

The present study focused on the three species of electric rays known to occur in the Mediterranean Sea: Torpedo torpedo, Torpedo marmorata and Tetronarce nobiliana. Correct identification of specimens is needed to properly assess the impact of fisheries on populations and species. Unfortunately, torpedoes share high morphological similarities, boosting episodes of field misidentification. In this context, genetic data was used (1) to identify specimens caught during fishing operations, (2) to measure the diversity among and within these species, and (3) to shed light on the possible occurrence of additional hidden species in the investigated area. New and already published sequences of COI and NADH2 mitochondrial genes were analyzed, both at a small scale along the Sardinian coasts (Western Mediterranean) and at a large scale in the whole Mediterranean Sea. High levels of genetic diversity were found in Sardinian populations, being significantly different from other areas of the Eastern Mediterranean Sea due to the biotic and abiotic factors here discussed. Sardinian torpedoes can hence be indicated as priority populations/areas to be protected within the Mediterranean Sea. Moreover, sequence data confirmed that only the three species occur in the investigated area. The application of several ‘species-delimitation’ methods found evidence of cryptic species in the three species outside the Mediterranean Sea, as well as in other genera/families, suggesting the urgent need for future studies and a comprehensive revision of the order Torpediniformes for its effective conservation. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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18 pages, 5373 KiB

Open AccessArticle

Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers

by Di Wei, Sichen Zheng, Songlin Wang, Jingkai Yan, Zhihong Liu, Liqing Zhou, Biao Wu and Xiujun Sun

Animals 2023, 13(18), 2886; https://doi.org/10.3390/ani13182886 - 11 Sep 2023

Cited by 2 | Viewed by 1069

Abstract

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand [...] Read more.

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean F_ST of the total population was 0.4534). Pairwise F_ST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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18 pages, 2102 KiB

Open AccessArticle

Matching an Old Marine Paradigm: Limitless Connectivity in a Deep-Water Fish over a Large Distance

by Alice Ferrari, Martina Spiga, Miriam Dominguez Rodriguez, Fabio Fiorentino, Juan Gil-Herrera, Pilar Hernandez, Manuel Hidalgo, Carolina Johnstone, Sana Khemiri, Kenza Mokhtar-Jamaï, Irene Nadal, Montse Pérez, Simone Sammartino, Marcelo Vasconcellos and Alessia Cariani

Animals 2023, 13(17), 2691; https://doi.org/10.3390/ani13172691 - 23 Aug 2023

Cited by 1 | Viewed by 1184

Abstract

Investigations of population structuring in wild species are fundamental to complete the bigger picture defining their ecological and biological roles in the marine realm, to estimate their recovery capacity triggered by human disturbance and implement more efficient management strategies for fishery resources. The [...] Read more.

Investigations of population structuring in wild species are fundamental to complete the bigger picture defining their ecological and biological roles in the marine realm, to estimate their recovery capacity triggered by human disturbance and implement more efficient management strategies for fishery resources. The Blackspot Seabream (Pagellus bogaraveo, Brünnich 1768) is a commercially valuable deep-water fish highly exploited over past decades. Considering its exploitation status, deepening the knowledge of intraspecific variability, genetic diversity, and differentiation using high-performing molecular markers is considered an important step for a more effective stock assessment and fishery management. With one of the largest efforts conceived of and completed by countries overlooking the Atlantic and Mediterranean coasts in recent years, a total of 320 individuals were collected from different fishing grounds in the Mediterranean Sea and Atlantic Ocean and analysed using 29 microsatellite loci. We applied multiple statistical approaches to investigate the species’ connectivity and population structure across most of its described distribution area. Considering the incomplete knowledge regarding the migratory behaviour of adults, here we suggest the importance of egg and larval dispersal in sustaining the observed genetic connectivity on such a large geographical scale. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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16 pages, 726 KiB

Open AccessArticle

Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets

by Edgardo Díaz-Ferguson, Magaly Chial, Maribel Gonzalez, Edgardo Muñoz, Olga Chen, Ovidio Durán, Angel Javier Vega and Carlos Ramos Delgado

Animals 2023, 13(14), 2272; https://doi.org/10.3390/ani13142272 - 12 Jul 2023

Cited by 1 | Viewed by 1181

Abstract

Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of [...] Read more.

Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima’s D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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9 pages, 1079 KiB

Open AccessArticle

Occurrence of Aeromonas Species in the Cutaneous Mucus of Barbour’s Seahorses (Hippocampus barbouri) as Revealed by High-Throughput Sequencing

by Rose Chinly Mae H. Ortega, Sharon Rose M. Tabugo, Joey Genevieve T. Martinez, Chinee S. Padasas and José L. Balcázar

Animals 2023, 13(7), 1241; https://doi.org/10.3390/ani13071241 - 03 Apr 2023

Viewed by 1589

Abstract

Although several studies have described the bacterial community composition associated with marine fish, there is limited information related to seahorses. Moreover, previous studies have demonstrated that the skin microbiota is useful for determining health status and common disorders in the host. This study, [...] Read more.

Although several studies have described the bacterial community composition associated with marine fish, there is limited information related to seahorses. Moreover, previous studies have demonstrated that the skin microbiota is useful for determining health status and common disorders in the host. This study, therefore, aimed to explore the skin bacterial community composition in Barbour’s seahorse (Hippocampus barbouri) using high-throughput sequencing of 16S ribosomal RNA genes. Water and sediment samples from the surrounding environment were also analyzed for comparative purposes. The results revealed that sequences affiliated with the Shewanellaceae family were dominant in the skin of female Barbour’s seahorses and sediment samples, whereas sequences affiliated with the Bacillaceae family were dominant in the skin of male Barbour’s seahorses. Interestingly, sequences affiliated with the Aeromonas genus were found in the skin of Barbour’s seahorses, whose abundance was slightly similar between the female and male specimens. Further comparative analysis showed that the presence of Aeromonas species in the skin of Barbour’s seahorses was strongly influenced by the surrounding sediment. Given that some Aeromonas species are known to be important pathogens in humans and fish, these results may be used for further research on the dependency of the skin microbial composition on the environment as well as determine whether the presence of Aeromonas and other detected species has implications on seahorse health. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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17 pages, 2775 KiB

Open AccessArticle

Genomic Characterization of hox Genes in Senegalese Sole (Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes

by Marco Mendizábal-Castillero, Manuel Alejandro Merlo, Ismael Cross, María Esther Rodríguez and Laureana Rebordinos

Animals 2022, 12(24), 3586; https://doi.org/10.3390/ani12243586 - 19 Dec 2022

Cited by 1 | Viewed by 1599

Abstract

The Senegalese sole (Solea senegalensis, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high [...] Read more.

The Senegalese sole (Solea senegalensis, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high mortality during the larval and juvenile phase. The study aims to characterize the hox gene clusters in S. senegalensis to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain hox genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the hox clusters were studied by sequence analysis, comparative genomics, and cytogenetic and phylogenetic analysis. Cytogenetic analysis demonstrated the localization of four BAC clones on chromosome pairs 4, 12, 13, and 16 of the Senegalese sole cytogenomic map. Comparative and phylogenetic analysis showed a highly conserved organization in each cluster and different phylogenetic clustering in each hox cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the hoxba cluster, mainly retroelements. Therefore, a possible loss of the hoxb7a gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of hox clusters to be understood, and is a good base for further studies of expression patterns. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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Review

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31 pages, 6934 KiB

Open AccessReview

Review: Recent Applications of Gene Editing in Fish Species and Aquatic Medicine

by Anikó Gutási, Sabine E. Hammer, Mansour El-Matbouli and Mona Saleh

Animals 2023, 13(7), 1250; https://doi.org/10.3390/ani13071250 - 04 Apr 2023

Cited by 4 | Viewed by 4548

Abstract

Gene editing and gene silencing techniques have the potential to revolutionize our knowledge of biology and diseases of fish and other aquatic animals. By using such techniques, it is feasible to change the phenotype and modify cells, tissues and organs of animals in [...] Read more.

Gene editing and gene silencing techniques have the potential to revolutionize our knowledge of biology and diseases of fish and other aquatic animals. By using such techniques, it is feasible to change the phenotype and modify cells, tissues and organs of animals in order to cure abnormalities and dysfunctions in the organisms. Gene editing is currently experimental in wide fields of aquaculture, including growth, controlled reproduction, sterility and disease resistance. Zink finger nucleases, TALENs and CRISPR/Cas9 targeted cleavage of the DNA induce favorable changes to site-specific locations. Moreover, gene silencing can be used to inhibit the translation of RNA, namely, to regulate gene expression. This methodology is widely used by researchers to investigate genes involved in different disorders. It is a promising tool in biotechnology and in medicine for investigating gene function and diseases. The production of food fish has increased markedly, making fish and seafood globally more popular. Consequently, the incidence of associated problems and disease outbreaks has also increased. A greater investment in new technologies is therefore needed to overcome such problems in this industry. To put it concisely, the modification of genomic DNA and gene silencing can comprehensively influence aquatic animal medicine in the future. On the ethical side, these precise genetic modifications make it more complicated to recognize genetically modified organisms in nature and can cause several side effects through created mutations. The aim of this review is to summarize the current state of applications of gene modifications and genome editing in fish medicine. Full article

(This article belongs to the Special Issue Genetic and Genomic Advances in Fisheries and Aquaculture)

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