Genes

Research

34 pages, 6258 KiB

Open AccessArticle

Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production

by Simo Njabulo Maduna, Ólöf Dóra Bartels Jónsdóttir, Albert Kjartan Dagbjartarson Imsland, Davíð Gíslason, Patrick Reynolds, Lauri Kapari, Thor Arne Hangstad, Kristian Meier and Snorre B. Hagen

Genes 2023, 14(10), 1870; https://doi.org/10.3390/genes14101870 - 26 Sep 2023

Viewed by 2108

Abstract

Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate [...] Read more.

Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype–environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our ‘global’ sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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12 pages, 1854 KiB

Open AccessArticle

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

by Francesca Bertolini, Anisa Ribani, Fabrizio Capoccioni, Luca Buttazzoni, Samuele Bovo, Giuseppina Schiavo, Massimo Caggiano, Max F. Rothschild and Luca Fontanesi

Genes 2023, 14(4), 839; https://doi.org/10.3390/genes14040839 - 30 Mar 2023

Viewed by 2268

Abstract

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to [...] Read more.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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18 pages, 2842 KiB

Open AccessArticle

Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species

by David L. J. Vendrami, Joseph I. Hoffman and Craig S. Wilding

Genes 2023, 14(1), 14; https://doi.org/10.3390/genes14010014 - 21 Dec 2022

Cited by 1 | Viewed by 2262

Abstract

Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria–Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of [...] Read more.

Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria–Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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13 pages, 2713 KiB

Open AccessArticle

Complete Mitochondrial Genome of Two Ectoparasitic Capsalids (Platyhelminthes: Monogenea: Monopisthocotylea): Gene Content, Composition, and Rearrangement

by Changping Yang, Binbin Shan, Yan Liu, Liangming Wang, Qiaer Wu, Zhengli Luo and Dianrong Sun

Genes 2022, 13(8), 1376; https://doi.org/10.3390/genes13081376 - 1 Aug 2022

Cited by 2 | Viewed by 2173

Abstract

The capsalid monogeneans are important pathogens that generally infect marine fishes and have a substantial impact on fish welfare in aquaculture systems worldwide. However, the current mitogenome information on capsalids has received little attention, limiting the understanding of their evolution and phylogenetic relationships [...] Read more.

The capsalid monogeneans are important pathogens that generally infect marine fishes and have a substantial impact on fish welfare in aquaculture systems worldwide. However, the current mitogenome information on capsalids has received little attention, limiting the understanding of their evolution and phylogenetic relationships with other monogeneans. This paper reports the complete mitochondrial genomes of Capsala katsuwoni and Capsala martinieri for the first time, which we obtained using a next-generation sequencing method. The mitogenomes of C. katsuwoni and C. martinieri are 13,265 and 13,984 bp in length, respectively. Both species contain the typical 12 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The genome compositions show a moderate A+T bias (66.5% and 63.9% for C. katsuwoni and C. martinieri, respectively) and exhibit a negative AT skew but a positive GC skew in both species. One gene block rearrangement was found in C. katsuwoni in comparison with other capsalid species. Instead of being basal to the Gyrodactylidea and Dactylogyridea or being clustered with Dactylogyridea, all species of Capsalidea are grouped into a monophyletic clade. Our results clarify the gene rearrangement process and evolutionary status of Capsalidae and lay a foundation for further phylogenetic studies of monogeneans. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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15 pages, 1922 KiB

Open AccessArticle

Identification of Ancestry Informative Markers in Mediterranean Trout Populations of Molise (Italy): A Multi-Methodological Approach with Machine Learning

by Giovanna Salvatore, Valentino Palombo, Stefano Esposito, Nicolaia Iaffaldano and Mariasilvia D’Andrea

Genes 2022, 13(8), 1351; https://doi.org/10.3390/genes13081351 - 28 Jul 2022

Cited by 2 | Viewed by 1888

Abstract

Brown trout (Salmo trutta), like many other freshwater species, is threated by the release in its natural environment of alien species and the restocking with allochthonous conspecific stocks. Many conservation projects are ongoing and several morphological and genetic tools have been [...] Read more.

Brown trout (Salmo trutta), like many other freshwater species, is threated by the release in its natural environment of alien species and the restocking with allochthonous conspecific stocks. Many conservation projects are ongoing and several morphological and genetic tools have been proposed to support activities aimed to restore genetic integrity status of native populations. Nevertheless, due to the complexity of degree of introgression reached up after many generations of crossing, the use of dichotomous key and molecular markers, such as mtDNA, LDH-C1* and microsatellites, are often not sufficient to discriminate native and admixed specimens at individual level. Here we propose a reduced panel of ancestry-informative SNP markers (AIMs) to support on field activities for Mediterranean trout management and conservation purpose. Starting from the genotypes data obtained on specimens sampled in the main two Molise’s rivers (Central-Southern Italy), a 47 AIMs panel was identified and validated on simulated and real hybrid population datasets, mainly through a Machine Learning approach based on Random Forest classifier. The AIMs panel proposed may represent an interesting and cost-effective tool for monitoring the level of introgression between native and allochthonous trout population for conservation purpose and this methodology could be also applied in other species. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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17 pages, 2536 KiB

Open AccessArticle

Genetic Demography of the Blue and Red Shrimp, Aristeus antennatus: A Female-Based Case Study Integrating Multilocus Genotyping and Morphometric Data

by Alba Abras, Jose-Luis García-Marín, Sandra Heras, Melania Agulló, Manuel Vera, Laia Planella and María Inés Roldán

Genes 2022, 13(7), 1186; https://doi.org/10.3390/genes13071186 - 1 Jul 2022

Cited by 1 | Viewed by 1671

Abstract

In this study, we quantified the three key biological processes, growth, recruitment, and dispersal pattern, which are necessary for a better understanding of the population dynamics of the blue and red shrimp Aristeus antennatus. This marine exploited crustacean shows sex-related distribution along [...] Read more.

In this study, we quantified the three key biological processes, growth, recruitment, and dispersal pattern, which are necessary for a better understanding of the population dynamics of the blue and red shrimp Aristeus antennatus. This marine exploited crustacean shows sex-related distribution along the water column, being females predominate in the middle slope. The present study attempts to fill the existing gap in the females’ genetic demography, as scarce knowledge is available despite being the most abundant sex in catches. We analyzed morphometric data and genotyped 12 microsatellite loci in 665 A. antennatus females collected in two consecutive seasons, winter and summer 2016, at the main Mediterranean fishing ground as a model. Almost every female in summer was inseminated. Five modal groups were observed in both seasons, from 0+ to 4+ in winter and from 1+ to 5+ in summer. Commercial-sized sorting based on fishermen’s experience resulted in a moderate-to-high assertive method concerning cohort determination. Genetic data pointed out females’ horizontal movement between neighboring fishing grounds, explaining the low genetic divergence detected among western Mediterranean grounds. Our results could represent critical information for the future implementation of management measures to ensure long-time conservation of the A. antennatus populations. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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18 pages, 8158 KiB

Open AccessArticle

The Relative Power of Structural Genomic Variation versus SNPs in Explaining the Quantitative Trait Growth in the Marine Teleost Chrysophrys auratus

by Mike Ruigrok, Bing Xue, Andrew Catanach, Mengjie Zhang, Linley Jesson, Marcus Davy and Maren Wellenreuther

Genes 2022, 13(7), 1129; https://doi.org/10.3390/genes13071129 - 23 Jun 2022

Cited by 3 | Viewed by 2394

Abstract

Background: Genetic diversity provides the basic substrate for evolution. Genetic variation consists of changes ranging from single base pairs (single-nucleotide polymorphisms, or SNPs) to larger-scale structural variants, such as inversions, deletions, and duplications. SNPs have long been used as the general currency for [...] Read more.

Background: Genetic diversity provides the basic substrate for evolution. Genetic variation consists of changes ranging from single base pairs (single-nucleotide polymorphisms, or SNPs) to larger-scale structural variants, such as inversions, deletions, and duplications. SNPs have long been used as the general currency for investigations into how genetic diversity fuels evolution. However, structural variants can affect more base pairs in the genome than SNPs and can be responsible for adaptive phenotypes due to their impact on linkage and recombination. In this study, we investigate the first steps needed to explore the genetic basis of an economically important growth trait in the marine teleost finfish Chrysophrys auratus using both SNP and structural variant data. Specifically, we use feature selection methods in machine learning to explore the relative predictive power of both types of genetic variants in explaining growth and discuss the feature selection results of the evaluated methods. Methods: SNP and structural variant callers were used to generate catalogues of variant data from 32 individual fish at ages 1 and 3 years. Three feature selection algorithms (ReliefF, Chi-square, and a mutual-information-based method) were used to reduce the dataset by selecting the most informative features. Following this selection process, the subset of variants was used as features to classify fish into small, medium, or large size categories using KNN, naïve Bayes, random forest, and logistic regression. The top-scoring features in each feature selection method were subsequently mapped to annotated genomic regions in the zebrafish genome, and a permutation test was conducted to see if the number of mapped regions was greater than when random sampling was applied. Results: Without feature selection, the prediction accuracies ranged from 0 to 0.5 for both structural variants and SNPs. Following feature selection, the prediction accuracy increased only slightly to between 0 and 0.65 for structural variants and between 0 and 0.75 for SNPs. The highest prediction accuracy for the logistic regression was achieved for age 3 fish using SNPs, although generally predictions for age 1 and 3 fish were very similar (ranging from 0–0.65 for both SNPs and structural variants). The Chi-square feature selection of SNP data was the only method that had a significantly higher number of matches to annotated genomic regions of zebrafish than would be explained by chance alone. Conclusions: Predicting a complex polygenic trait such as growth using data collected from a low number of individuals remains challenging. While we demonstrate that both SNPs and structural variants provide important information to help understand the genetic basis of phenotypic traits such as fish growth, the full complexities that exist within a genome cannot be easily captured by classical machine learning techniques. When using high-dimensional data, feature selection shows some increase in the prediction accuracy of classification models and provides the potential to identify unknown genomic correlates with growth. Our results show that both SNPs and structural variants significantly impact growth, and we therefore recommend that researchers interested in the genotype–phenotype map should strive to go beyond SNPs and incorporate structural variants in their studies as well. We discuss how our machine learning models can be further expanded to serve as a test bed to inform evolutionary studies and the applied management of species. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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14 pages, 1469 KiB

Open AccessArticle

Population Genetic Structure of Marine Leech, Pterobdella arugamensis in Indo-West Pacific Region

by Syakirah Azmey, Hussein Taha, Gunanti Mahasri, Muhamad Amin, Ahasan Habib, Min Pau Tan and Takaomi Arai

Genes 2022, 13(6), 956; https://doi.org/10.3390/genes13060956 - 26 May 2022

Cited by 3 | Viewed by 3350

Abstract

Grouper aquaculture is rapidly expanding in both tropical and subtropical regions. The presence of marine leeches (Pterobdella arugamensis; previously named Zeylanicobdella arugamensis) infesting cultured groupers, however, can have a fatal effect on grouper aquaculture production and cause significant economic loss. [...] Read more.

Grouper aquaculture is rapidly expanding in both tropical and subtropical regions. The presence of marine leeches (Pterobdella arugamensis; previously named Zeylanicobdella arugamensis) infesting cultured groupers, however, can have a fatal effect on grouper aquaculture production and cause significant economic loss. Understanding the marine leech’s population structure is therefore important to determine its possible distributional origin and distributional mechanisms, which will help monitor and mitigate the infestation. In this study, a total of 84 marine leeches collected from cultured hybrid groupers Epinephelus spp. in Brunei Darussalam, Malaysia and Indonesia were identified as P. arugamensis, based on morphological and mitochondrial cytochrome c oxidase subunit I gene sequence analyses. These leech samples, together with additional sequences from the GenBank database, were grouped into four genetically distinct haplogroups: (1) Asia Pacific, (2) Borneo, (3) Surabaya and (4) Iran. The four populations were found to be highly diverged from each other. The results also suggested that the samples from the Asia Pacific population could be dispersed and transported from Indonesia. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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13 pages, 2399 KiB

Open AccessEditor’s ChoiceArticle

Evaluation of Immune Status in Two Cohorts of Atlantic Salmon Raised in Different Aquaculture Systems (Case Study)

by Hege Lund, Anne Bakke, Preben Boysen, Sergey Afanasyev, Alexander Rebl, Farah Manji, Gordon Ritchie and Aleksei Krasnov

Genes 2022, 13(5), 736; https://doi.org/10.3390/genes13050736 - 22 Apr 2022

Cited by 6 | Viewed by 3478

Abstract

Assessment of immune competence of farmed Atlantic salmon is especially important during smoltification and the first several months in the sea. Recently developed tools were applied to salmon raised in a traditional flow-through facility (FT, cohort 1) and in a recirculation aquaculture system [...] Read more.

Assessment of immune competence of farmed Atlantic salmon is especially important during smoltification and the first several months in the sea. Recently developed tools were applied to salmon raised in a traditional flow-through facility (FT, cohort 1) and in a recirculation aquaculture system (RAS, cohort 2). Fish were sampled at four time-points: parr, smolt, and at three weeks and three months after seawater transfer (SWT); expression of 85 selected immune and stress genes, IgM transcripts (Ig-seq), and circulating antibodies were analyzed. A steady increase in gene expression was seen over time in gill and spleen in both cohorts, and especially in antiviral and inflammatory genes in the gill. Differences between the cohorts were greatest in the dorsal fin but later leveled off. Comparison with a gill reference dataset found a deviation in only three of 85 fish, suggesting a good immune status in both cohorts. Levels of both specific and nonspecific antibodies were higher in cohort 2 in smolts and in growers three weeks after SWT; however, levels evened out after three months in the sea. Ig-seq indicated association between antibody production, expansion of the largest clonotypes, and massive migration of B cells from spleen to gill in smolts. The results suggested greater agitation and higher reactivity of the immune system in RAS-produced salmon, but the difference between the cohorts leveled off over time. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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16 pages, 1526 KiB

Open AccessArticle

Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers

by Adrián Casanova, Sandra Heras, Alba Abras, María Inés Roldán, Carmen Bouza, Manuel Vera, José Luis García-Marín and Paulino Martínez

Genes 2022, 13(2), 255; https://doi.org/10.3390/genes13020255 - 28 Jan 2022

Cited by 6 | Viewed by 3503

Abstract

Brown trout (Salmo trutta L.) populations have been restocked during recent decades to satisfy angling demand and counterbalance the decline of wild populations. Millions of fertile brown trout individuals were released into Mediterranean and Atlantic rivers from hatcheries with homogeneous central European [...] Read more.

Brown trout (Salmo trutta L.) populations have been restocked during recent decades to satisfy angling demand and counterbalance the decline of wild populations. Millions of fertile brown trout individuals were released into Mediterranean and Atlantic rivers from hatcheries with homogeneous central European stocks. Consequently, many native gene pools have become endangered by introgressive hybridization with those hatchery stocks. Different genetic tools have been used to identify and evaluate the degree of introgression starting from pure native and restocking reference populations (e.g., LDH-C* locus, microsatellites). However, due to the high genetic structuring of brown trout, the definition of the "native pool" is hard to achieve. Additionally, although the LDH-C* locus is useful for determining the introgression degree at the population level, its consistency at individual level is far from being accurate, especially after several generations were since releases. Accordingly, the development of a more powerful and cost-effective tool is essential for an appropriate monitoring to recover brown-trout-native gene pools. Here, we used the 2b restriction site-associated DNA sequencing (2b-RADseq) and Stacks 2 with a reference genome to identify single-nucleotide polymorphisms (SNPs) diagnostic for hatchery-native fish discrimination in the Atlantic and Mediterranean drainages of the Iberian Peninsula. A final set of 20 SNPs was validated in a MassARRAY® System genotyping by contrasting data with the whole SNP dataset using samples with different degree of introgression from those previously recorded. Heterogeneous introgression impact was confirmed among and within river basins, and was the highest in the Mediterranean Slope. The SNP tool reported here should be assessed in a broader sample scenario in Southern Europe considering its potential for monitoring recovery plans. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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13 pages, 1073 KiB

Open AccessArticle

Selection of References for microRNA Quantification in Japanese Flounder (Paralichthys olivaceus) Normal Tissues and Edwardsiella tarda-Infected Livers

by Saisai Liu, Haofei Song, Zeyu Liu, Wei Lu, Quanqi Zhang and Jie Cheng

Genes 2022, 13(2), 175; https://doi.org/10.3390/genes13020175 - 19 Jan 2022

Cited by 3 | Viewed by 2114

Abstract

MicroRNA (miRNA) plays essential roles in post-transcriptional regulation of protein coding genes, and the quantitative real-time polymerase chain reaction (qRT-PCR) is the powerful and broadly employed tool to conduct studies of miRNA expression. Identifying appropriate references to normalize quantitative data is a prerequisite [...] Read more.

MicroRNA (miRNA) plays essential roles in post-transcriptional regulation of protein coding genes, and the quantitative real-time polymerase chain reaction (qRT-PCR) is the powerful and broadly employed tool to conduct studies of miRNA expression. Identifying appropriate references to normalize quantitative data is a prerequisite to ensure the qRT-PCR accuracy. Until now, there has been no report about miRNA reference for qRT-PCR in Japanese flounder (Paralichthys olivaceus), one important marine cultured fish along the coast of Northern Asia. In this study, combined with miRNA-Seq analysis and literature search, 10 candidates (miR-34a-5p, miR-205-5p, miR-101a-3p, miR-22-3p, miR-23a-3p, miR-210-5p, miR-30c-5p, U6, 5S rRNA, and 18S rRNA) were chosen as potential references to test their expression stability among P. olivaceus tissues, and in livers of P. olivaceus infected with Edwardsiella tarda at different time points. The expression stability of these candidates was analyzed by qRT-PCR and evaluated with Delta CT, BestKeeper, geNorm, as well as NormFinder methods, and RefFinder was employed to estimate the comprehensive ranking according to the four methods. As the result, miR-22-3p and miR-23a-3p were proved to be the suitable combination as reference miRNAs for both P. olivaceus normal tissues and livers infected with E. tarda, and they were successfully applied to normalize miR-7a and miR-221-5p expression in P. olivaceus livers in response to E. tarda infection. All these results provide valuable information for P. olivaceus miRNA quantitative expression analysis in the future. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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23 pages, 3055 KiB

Open AccessFeature PaperArticle

Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan

by Che-Chun Chen, Chang-Wen Huang, Chung-Yen Lin, Chia-Hui Ho, Hong Nhat Pham, Te-Hua Hsu, Tzu-Tang Lin, Rong-Hwa Chen, Shuenn-Der Yang, Chin-I. Chang and Hong-Yi Gong

Genes 2022, 13(1), 99; https://doi.org/10.3390/genes13010099 - 31 Dec 2021

Cited by 11 | Viewed by 4578

Abstract

There are numerous means to improve the tilapia aquaculture industry, and one is to develop disease resistance through selective breeding using molecular markers. In this study, 11 disease-resistance-associated microsatellite markers including 3 markers linked to hamp2, 4 linked to hamp1, 1 [...] Read more.

There are numerous means to improve the tilapia aquaculture industry, and one is to develop disease resistance through selective breeding using molecular markers. In this study, 11 disease-resistance-associated microsatellite markers including 3 markers linked to hamp2, 4 linked to hamp1, 1 linked to pgrn2, 2 linked to pgrn1, and 1 linked to piscidin 4 (TP4) genes were established for tilapia strains farmed in Taiwan after challenge with Streptococcus inae. The correlation analysis of genotypes and survival revealed a total of 55 genotypes related to survival by the chi-square and Z-test. Although fewer markers were found in B and N2 strains compared with A strain, they performed well in terms of disease resistance. It suggested that this may be due to the low potency of some genotypes and the combinatorial arrangement between them. Therefore, a predictive model was built by the genotypes of the parental generation and the mortality rate of different combinations was calculated. The results show the same trend of predicted mortality in the offspring of three new disease-resistant strains as in the challenge experiment. The present findings is a nonkilling method without requiring the selection by challenge with bacteria or viruses and might increase the possibility of utilization of selective breeding using SSR markers in farms. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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17 pages, 920 KiB

Open AccessArticle

Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus)

by Jean-Paul Baesjou and Maren Wellenreuther

Genes 2021, 12(11), 1737; https://doi.org/10.3390/genes12111737 - 29 Oct 2021

Cited by 9 | Viewed by 2681

Abstract

Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help [...] Read more.

Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of F_ST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations F_ST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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15 pages, 3120 KiB

Open AccessArticle

MicroRNAs May Play an Important Role in Sexual Reversal Process of Chinese Soft-Shelled Turtle, Pelodiscus sinensis

by Tong Zhou, Hang Sha, Meng Chen, Guobin Chen, Guiwei Zou and Hongwei Liang

Genes 2021, 12(11), 1696; https://doi.org/10.3390/genes12111696 - 25 Oct 2021

Cited by 9 | Viewed by 2981

Abstract

The Chinese soft-shelled (Pelodiscus sinensis) turtle exhibits obvious sex dimorphism, which leads to the higher economic and nutritional value of male individuals. Exogenous hormones can cause the transformation from male to female phenotype during gonadal differentiation. However, the molecular mechanism related [...] Read more.

The Chinese soft-shelled (Pelodiscus sinensis) turtle exhibits obvious sex dimorphism, which leads to the higher economic and nutritional value of male individuals. Exogenous hormones can cause the transformation from male to female phenotype during gonadal differentiation. However, the molecular mechanism related to the sexual reversal process is unclear. In this study, we compared the difference between the small RNAs of male, female, and pseudo-female turtles by small RNA-seq to understand the sexual reversal process of Chinese soft-shelled turtles. A certain dose of estrogen can cause the transformation of Chinese soft-shelled turtles from male to female, which are called pseudo-female individuals. The result of small RNA-seq has revealed that the characteristics of pseudo-females are very similar to females, but are strikingly different from males. The number of the microRNAs (miRNAs) of male individuals was significantly less than the number of female individuals or pseudo-female individuals, while the expression level of miRNAs of male individuals were significantly higher than the other two types. Furthermore, we found 533 differentially expressed miRNAs, including 173 up-regulated miRNAs and 360 down-regulated miRNAs, in the process of transformation from male to female phenotype. Cluster analysis of the total 602 differential miRNAs among females, males, and pseudo-females showed that miRNAs played a crucial role during the sexual differentiation. Among these differential miRNAs, we found 12 miRNAs related to gonadal development and verified their expression by qPCR. The TR-qPCR results confirmed the differential expression of 6 of the 12 miRNAs: miR-26a-5p, miR-212-5p, miR-202-5p, miR-301a, miR-181b-3p and miR-96-5p were involved in sexual reversal process, which was consistent with the results of omics. Using these six miRNAs and some of their target genes, we constructed a network diagram related to gonadal development. We suggest that these miRNAs may play an important role in the process of effective sex reversal, which would contribute to the breeding of all male strains of Chinese soft-shelled turtles. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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18 pages, 22903 KiB

Open AccessArticle

Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America

by Josue Chinchilla-Vargas, Jonathan R. Meerbeek, Max F. Rothschild and Francesca Bertolini

Genes 2021, 12(7), 1021; https://doi.org/10.3390/genes12071021 - 30 Jun 2021

Viewed by 2719

Abstract

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of [...] Read more.

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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Review

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20 pages, 2181 KiB

Open AccessReview

Parvalbumin: A Major Fish Allergen and a Forensically Relevant Marker

by Subham Mukherjee, Petra Horka, Kamila Zdenkova and Eliska Cermakova

Genes 2023, 14(1), 223; https://doi.org/10.3390/genes14010223 - 14 Jan 2023

Cited by 16 | Viewed by 7717

Abstract

Parvalbumins (PVALBs) are low molecular weight calcium-binding proteins. In addition to their role in many biological processes, PVALBs play an important role in regulating Ca2+ switching in muscles with fast-twitch fibres in addition to their role in many biological processes. The PVALB gene [...] Read more.

Parvalbumins (PVALBs) are low molecular weight calcium-binding proteins. In addition to their role in many biological processes, PVALBs play an important role in regulating Ca2+ switching in muscles with fast-twitch fibres in addition to their role in many biological processes. The PVALB gene family is divided into two gene types, alpha (α) and beta (β), with the β gene further divided into two gene types, beta1 (β1) and beta2 (β2), carrying traces of whole genome duplication. A large variety of commonly consumed fish species contain PVALB proteins which are known to cause fish allergies. More than 95% of all fish-induced food allergies are caused by PVALB proteins. The authentication of fish species has become increasingly important as the seafood industry continues to grow and the growth brings with it many cases of food fraud. Since the PVALB gene plays an important role in the initiation of allergic reactions, it has been used for decades to develop alternate assays for fish identification. A brief review of the significance of the fish PVALB genes is presented in this article, which covers evolutionary diversity, allergic properties, and potential use as a forensic marker. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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35 pages, 588 KiB

Open AccessReview

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

by Artem P. Dysin, Yuri S. Shcherbakov, Olga A. Nikolaeva, Valerii P. Terletskii, Valentina I. Tyshchenko and Natalia V. Dementieva

Genes 2022, 13(12), 2221; https://doi.org/10.3390/genes13122221 - 27 Nov 2022

Cited by 5 | Viewed by 2971

Abstract

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic [...] Read more.

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

Other

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10 pages, 1078 KiB

Open AccessBrief Report

Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery

by J. Antonio Baeza, José Luis Molina-Quirós and Sebastián Hernández-Muñoz

Genes 2021, 12(11), 1710; https://doi.org/10.3390/genes12111710 - 27 Oct 2021

Cited by 5 | Viewed by 2694

Abstract

The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation [...] Read more.

The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, N. pectoralis is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in N. pectoralis. The haploid genome size estimated using a k-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in N. pectoralis consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic N. pectoralis. Full article

(This article belongs to the Special Issue Genomics in Aquaculture and Fisheries)

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