Establishment and application of distant hybridization technology in fish

Genomic and chromosomal architectures underlying fertility maintenance in the testes of intergeneric homoploid hybrids

The remarkable diversity of the Cyprinidae family highlights the importance of hybridization and gene flow in generating genetic variation, adaptation, and even speciation. However, why do cyprinid fish frequently overcome postzygotic reproductive isolation, a mechanism that normally prevents successful reproduction after fertilization? To address this gap in knowledge, we conducted comparative studies using reciprocal F1 hybrid lineages derived from intergeneric hybridization between the cyprinid species Megalobrama amblycephala and Culter alburnus. Utilizing long-read genome sequencing, ATAC-seq, Hi-C, and mRNA-seq technologies, we identified rapid genomic variations, chromatin remodeling, and gene expression changes in the testicular cells of F1 hybrid individuals. By analyzing the distribution of these alterations across three gene categories (allelic genes, orphan genes, and testis-specific genes), we found that changes were less pronounced in allelic and testis-specific genes but significantly more pronounced in orphan genes. Furthermore, we hypothesize that rnf212b is a crucial testis-specific gene that regulates spermatogenesis. Our findings suggest that allelic and testis-specific genes potentially mitigate "genomic shock" on reproductive function following hybridization. This research offers potential insights into the formation mechanisms of homoploid hybridization by demonstrating the coordinated interplay of genomic variations, chromatin remodeling, and gene expression changes during testicular development and spermatogenesis.

Exploring the role of miR-430 in hybrid fish during embryonic development

miR-430, a microRNA expressed at the maternal-zygotic transition (MZT) stage, plays a vital role in maternal transcript clearance and suppression of primordial germ cell-specific genes. This study investigated the expression and regulation of miR-430 in goldfish (Carassius auratus var., ♀) × rare gudgeon (Gobiocypris rarus, ♂) [s-GFRG, survival] and rare gudgeon (♀) × goldfish (♂) [d-RGGF, death] embryos to explore the role of miR-430 in hybrid fish. Gene sequence comparisons demonstrated that three types of miR-430 in s-GFRG exhibited similarity to that of the female parent goldfish (GF) and displayed characteristic variation. Conversely, d-RGGF exhibited two miR-430 variants resembling those of GF and rare gudgeon (RG). In addition, real-time quantitative PCR and whole-mount in situ hybridization revealed that the expression trend of miR-430 was the same in hybrid progenies, and temporal expression was delayed compared to that in the parental embryos. However, miR-430 expression was significantly lower in d-RGGF than in GF and s-GFRG embryos. Similar to the development of d-RGGF embryos, miR-430-silenced s-GFRG embryos exhibited morphological abnormalities including spinal curvature and pericardial cavity enlargement. Overexpression of miR-430 in d-RGGF embryos effectively rescued somitogenesis and prolonged fry survival. Thus, an abnormal MZT resulting from disturbed miR-430 expression may contribute to hybrid embryo mortality.

Comparative Analysis of Genetic Structure and Diversity in Larimichthys polyactis, Larimichthys crocea, and Their Reciprocal Hybrids Based on Microsatellite Loci

In this study, we compared the genetic diversity and structure of small yellow croaker (Larimichthys polyactis, LP), large yellow croaker (Larimichthys crocea, LC), and their reciprocal hybrids (LP ♀ × LC ♂ (LCP) and LC ♀ × LP ♂ (LPC)) using 14 microsatellite loci. Our results revealed that genetic diversity was highest in LCP, followed by LP and LPC, with LC exhibiting the lowest level. Additionally, among the two hybrid progenies, the number of loci in LCP deviating from Hardy-Weinberg equilibrium was lower. This suggests that LCP is a more appropriate choice as breeding material and has the potential to enhance germplasm resources. Based on the analysis of 14 microsatellite loci, we observed that both hybrid species clustered with their respective maternal parents. Specifically, LPC exhibited a closer genetic relationship to its maternal parent than LCP did. Furthermore, the majority of genes in LPC were inherited from its maternal parent (LP). In the LCP population, approximately 63% of individuals possessed gene profiles similar to those observed in LPC, while the remaining individuals displayed a mix from both parents. This study provides a strategic direction for the efficient utilization and management of novel germplasm resources in hybrid yellow croaker. Hybrid yellow croaker serves as an intermediate breeding material, playing a significant role in the genetic improvement of Larimichthys crocea and Larimichthys polyactis.

A vaccine combining ORF132 and ORF25 expressed by Saccharomyces cerevisiae induces protective immunity in Carassius auratus gibelio against CyHV-2

CyHV-2 is the pathogen of herpesvirus hematopoietic necrosis (HVHN), resulting in significant economic losses in crucian carp. Although multiple oral vaccines have been developed to prevent CyHV-2, they have not achieved ideal protective effects. To improve the protective effect of oral vaccine, a combination vaccine was conducted by mixing recombinant Saccharomyces cerevisiae displaying ORF132 or ORF25 on the cell surface in a 1:1 ratio. Oral immunization with this combined vaccine induced specific antibodies against ORF132 and ORF25 in fish serum, as well as increased the transcription levels of IgT, IgM, IL-1β, IFN-1, and TNF-α in the spleen, head-kidney, and hindgut. Importantly, the combined vaccine provided significant protection against CyHV-2 infection in crucian carp, resulting in a relative percent survival of 80.77 %. Additionally, it suppressed viral load and alleviated pathological damage of CyHV-2-infected fish. The results suggest that the combined vaccine exhibits a better protective effect compared to the single-antigen vaccines, indicating it as a promising approach to prevent CyHV-2 outbreaks.

Genomes reveal pervasive distant hybridization in nature among cyprinid fishes

BACKGROUND

Genomic data have unveiled a fascinating aspect of the evolutionary past, showing that the mingling of different species through hybridization has left its mark on the histories of numerous life forms. However, the relationship between hybridization events and the origins of cyprinid fishes remains unclear.

RESULTS

In this study, we generated de novo assembled genomes of 8 cyprinid fishes and conducted phylogenetic analyses on 24 species. Widespread allele sharing across species boundaries was observed within 7 subfamilies of cyprinid fishes. Based on a systematic analysis of multiple tissues, we found that the testis exhibited a conserved pattern of divergence between the herbivorous Megalobrama amblycephala and the carnivorous Culter alburnus, suggesting a potential link to incomplete reproductive isolation. Significant differences in the expression of 4 genes (dpp2, ctrl, psb7, and ppce) in the liver and intestine, accompanied by variations in enzyme activities, indicated swift divergence in digestive enzyme secretion. Moreover, we identified introgressed genes linked to organ development in sympatric fishes with analogous feeding habits within the Cultrinae and Leuciscinae subfamilies.

CONCLUSIONS

Our findings highlight the significant role played by incomplete reproductive isolation and frequent gene flow events, particularly those associated with the development of digestive organs, in driving speciation among cyprinid fishes in diverse freshwater ecosystems.

The phenotype, sex ratio and gonadal development in triploid hybrids of rainbow trout (Oncorhynchus mykiss) ♀ and brook trout (Salvelinus fontinalis) ♂

The phenotype, genetic sex ratio and gonadal development characteristics were evaluated in randomly selected juvenile (15 months old), sub-adult (22 months old) and adult (30 months old) triploid hybrids of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis). The examined fish originated from the family produced by application High Hydrostatic Pressure (HHP) shock (9500 psi for 5 minutes, applied 35 minutes post-fertilization at 10°C) to eggs stripped from five rainbow trout females and fertilized with sperm of two brook trout males. After hatching, all fish were reared under the same conditions for three years. The ploidy level and hybrid status of the fish were confirmed through cytogenetic analysis and DNA genotyping. Three distinct phenotypes; trout-like (Tr-l) phenotype, salmon-like (Sa-l) phenotype and intermediate (Tr/Sa-l) phenotype, with the following frequencies: f= 50.8 %, f= 31.7 % and f= 17.5 %, respectively, were observed among the sampled specimens. Genetic males exclusively detected among individuals with Tr-l phenotype developed macroscopically visible and histologically functional testes in their second year of life, representing the lowest value for the aquaculture production. A comparable proportion of males and females was recorded among individuals with Sa-l and Tr/Sa-l phenotypes. Males with these phenotypes developed macroscopically distinguishable and histologically functional testes in their third year of life. In the genetic males, underdeveloped intersex or completely reduced gonads were recorded. This study revealed that individuals with Sa-l phenotype represent the greatest value for commercial production because of their unique appearance and complete sterility (females) or delayed maturation observed only after reaching the market size (males).

Fish IL-26 collaborates with IL-10R2 and IL-20R1 to enhance gut mucosal barrier during the antibacterial innate immunity

IL-26 is a cytokine that is crucial for the maintenance and function of the gut mucosal barrier. IL-26 signaling pathway relies on a heterodimeric receptor complex, which is composed of two distinct subunits, IL-10R2 and IL-20R1. However, there are no reports on the antibacterial immunity of IL-26 and its receptors in fish. For this purpose, in this study we identified IL-26 and its receptors IL-10R2 and IL-20R1 in Carassius cuvieri × Carassius auratus red var. (named WR-IL-26, WR-IL10R2 and WR-IL20R1, respectively). Phylogenetic analysis confirmed the conservation of these genes, with shared structural motifs similar to those found in higher vertebrates. Upon exposure to Aeromonas hydrophila, a common fish pathogen, there was a significant upregulation of WR-IL-26, WR-IL10R2 and WR-IL20R1 in the gut, indicating a potential role in the immune response to infection. A co-immunoprecipitation assay revealed that WR-IL-26 formed complexes with WR-IL10R2 and WR-IL20R1. In vivo experiments demonstrated that administration of WR-IL-26 activated the JAK1-STAT3 signaling pathway and protected the gut mucosa barrier from A. hydrophila infection. Conversely, silencing WR-IL10R2 and WR-IL20R1 via RNA interference significantly attenuated the activation of WR-IL-26-mediated JAK1-STAT3 pathway. These results provided new insights into the role of IL-26 and its receptors in the gut mucosa barrier and could offer novel therapeutic strategies for managing bacterial infections in aquaculture.

Immersion immunization with recombinant Saccharomyces cerevisiae displaying ORF25 induced protective immunity against cyprinid herpesvirus 2

Displaying antigens on yeast surface as an oral vaccine has been widely explored, while its potential as an immersion vaccine has not been evaluated. Here, an immersion vaccine was prepared by displaying ORF25 of Cyprinid herpesvirus 2 (CyHV-2) on the surface of Saccharomyces cerevisiae. Carassius auratus gibelio was immersion immunized by 2 × 107 CFU/mL yeast for 2 h, and reinforce the immunity using the same method 14 days after the first immunization. The results showed that ORF25 specific antibody in immunized crucian carp serum was detected at a high level, and the mRNA expression level of IgM, IgT, IL-1β, and IFN-1 in vaccinated head-kidney and spleen tissues were higher than the control group, indicating that innate and adaptive immunity were induced. Moreover, the immersion vaccination provided effective protection for fish against CyHV-2, leading to a relative percent survival of 50.2%. Meanwhile, immersion vaccination restrained virus replication and histological damage in CyHV-2 infected crucian carp. Our data suggested that immersion immunization of S. cerevisiae-displayed ORF25 could be served as a candidate vaccine to prevent CyHV-2 infection.

Comparative Transcriptome Analysis of the Hypothalamic-Pituitary-Gonadal Axis of Jinhu Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus tukula ♂) and Tiger Grouper (Epinephelus fuscoguttatus)

Jinhu groupers, the hybrid offspring of tiger groupers (Epinephelus fuscoguttatus) and potato groupers (Epinephelus tukula), have excellent heterosis in fast growth and strong stress resistance. However, compared with the maternal tiger grouper, Jinhu groupers show delayed gonadal development. To explore the interspecific difference in gonadal development, we compared the transcriptomes of brain, pituitary, and gonadal tissues between Jinhu groupers and tiger groupers at 24-months old. In total, 3034 differentially expressed genes (DEGs) were obtained. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that the osteoclast differentiation, oocyte meiosis, and ovarian steroidogenesis may be involved in the difference in gonadal development. Trend analysis showed that the DEGs were mainly related to signal transduction and cell growth and death. Additionally, differences in expression levels of nr4a1, pgr, dmrta2, tbx19, and cyp19a1 may be related to gonadal retardation in Jinhu groupers. A weighted gene co-expression network analysis revealed three modules (i.e., saddlebrown, paleturquoise, and greenyellow) that were significantly related to gonadal development in the brain, pituitary, and gonadal tissues, respectively, of Jinhu groupers and tiger groupers. Network diagrams of the target modules were constructed and the respective hub genes were determined (i.e., cdh6, col18a1, and hat1). This study provides additional insight into the molecular mechanism underlying ovarian stunting in grouper hybrids.

Inherited anoxia tolerance and growth performance can result in enhanced invasiveness in hybrid fish

Northern hemisphere freshwater ecosystems are projected to experience significant warming and shortening of winter duration in this century. This change coupled with depletion of oxygen (hypoxia) will result in a shift toward fish species with higher optimal temperatures for growth and reproduction that can mitigate hypoxic stress. Here, we tested the assumption that reproduction between two distant species, i.e. anoxic-intolerant common carp (Cyprinus carpio) and anoxic-tolerant goldfish (Carassius auratus), results in the expression of genes responsible for ethanol synthesis (alcohol dehydrogenase and pyruvate dehydrogenase subunit E1β2). The expression of this ethanol-producing pyruvate decarboxylase pathway may transform the biochemical characteristics of progeny into anoxic-tolerant hybrids, expanding their suitable environmental range and potentially increasing invasiveness. Concurrently, a genetic strategy for improving fish tolerance to oxygen-depleted environments will be a valuable physiological trait in fish culture. Differential quantification of gene expression by analyzing mRNA revealed that, compared with koi×koi, koi female×goldfish male (F1 hybrid) possessed the pyruvate dehydrogenase subunit E1β2 gene construct, which was expressed at significantly greater levels in red muscle. The potential of this hybrid to both survive in extreme anoxic conditions and grow at elevated water temperatures would likely contribute to their ecological success.

Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based on cntd1 Knockout in Zebrafish

Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the cyclin N-terminal domain containing 1 (cntd1) using CRISPR/Cas9 technology. This resulted in impaired formation of meiotic crossovers, leading to cell-cycle arrest during meiotic metaphase and triggering apoptosis of spermatocytes in the testes. Despite these defects, the mutant (cntd1-/-) males were still able to produce a limited amount of sperm with normal ploidy and function. Interestingly, in the mutant females, it was the ploidy not the capacity of egg production that was altered. This resulted in the production of haploid, aneuploid, and unreduced gametes. This alteration enabled us to successfully obtain triploid and tetraploid zebrafish from cntd1-/- and cntd1-/-/- females, respectively. Furthermore, the tetraploid-heterozygous zebrafish produced reduced-diploid gametes and yielded all-triploid or all-tetraploid offspring when crossed with wild-type (WT) or tetraploid zebrafish, respectively. Collectively, our findings provide direct evidence supporting the crucial role of meiotic crossover defects in the process of polyploidization. This is particularly evident in the generation of unreduced eggs in fish and, potentially, other vertebrate species.

Evolutionarily conserved IL-22 participates in gut mucosal barrier through its receptors IL-22BP, IL-10R2 and IL-22RA1 during bacterial infection in teleost

IL-22 is a critical cytokine of epithelial mucosal barrier. In humans, IL-22 signals through a heteroduplex receptor consisting of IL-22R and IL-10Rβ. In fish, IL-22 and its receptors homologues have been cloned in a number of species, however, no studies have been reported how the receptors are involved in IL-22 transduction. For this purpose, in this study we identified IL-22 and its soluble receptor IL-22BP and transmembrane receptors IL-22RA1 and IL-10R2 in Carassius cuvieri × Carassius auratus red var. (named WR-IL-22, WR-IL-22BP, WR-IL10R2 and WR-IL22RA1, respectively). WR-IL-22, WR-IL-22BP, WR-IL10R2 and WR-IL22RA1 were relatively conserved in the evolutionary process, sharing the same conserved domains as their higher vertebrate homologues. When the fish were infected with the Aeromonas hydrophila, the expression of WR-IL-22, WR-IL-22BP, WR-IL10R2 and WR-IL22RA1 were significantly induced in the gut. The co-IP assay showed that WR-IL-22 not only interacted with WR-IL-22BP, but also with WR-IL10R2 and WR-IL22RA1. When introduced in vivo, WR-IL-22 activated the JAK1-STAT3 axis and protected the gut mucosa from A. hydrophila infection. However, overexpression of WR-IL-22BP or knockdown of transmembrane receptors WR-IL10R2 and WR-IL22RA1 significantly inhibited the activation of WR-IL-22-mediated JAK1-STAT3 axis and promoted bacterial colonization in the gut. These results provided new insights into the role of IL-22 and its receptors in the gut mucosa barrier and immune response in teleost.

Nonadditive and allele-specific expression of ghrelin in hybrid tilapia

Background

Interspecies hybridization is an important breeding method to generate fishes with heterosis in aquaculture. Using this method, hybrid Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (Oreochromis aureus, ♂) has been produced and widely farmed due to its growth and appetite superiorities. However, the genetic mechanism of these advanced traits is still not well understood. Ghrelin is a crucial gene that regulates growth and appetite in fishes. In the present study, we focused on the expression characteristics and its regulation of ghrelin in the hybrid.

Results

The tissue distribution analysis showed that ghrelin was predominantly expressed in the stomach in the hybrid. Ghrelin was more highly expressed in the stomach in the hybrid and Nile tilapia, compared to blue tilapia, showing a nonadditive pattern. Two single-nucleotide polymorphism (SNP) sites were identified including T/C and C/G from the second exon in the ghrelin gene from Nile tilapia and blue tilapia. By pyrosequencing based on the SNP sites, the allele-specific expression (ASE) of ghrelin in the hybrid was assayed. The result indicated that ghrelin in the hybrid showed higher maternal allelic transcript ratios. Fasting significantly increased ghrelin overall expression at 4, 8, 12, 24, and 48 h. In addition, higher maternal allelic transcript ratios were not changed in the fasting hybrids at 48 h. The cis and trans effects were determined by evaluating the overall expression and ASE values in the hybrid. The expression of ghrelin was mediated by compensating cis and trans effects in hybrid.

Conclusion

In summary, the present lines of evidence showed the nonadditive expression of ghrelin in the hybrid tilapia and its regulation by subgenomes, offering new insight into gene expression characteristics in hybrids.

WR-PTXF, a novel short pentraxin, protects gut mucosal barrier and enhances the antibacterial activity in Carassius cuvieri × Carassius auratus red var

The pentraxin family is an evolutionarily conserved group that plays an important role in innate immunity. C-reactive protein (CRP) and serum amyloid P component (SAP) are classical members of the short pentraxins and are known to be the major acute phase proteins. In this work, we have cloned a novel pentraxin fusion protein, WR-PTXF, from Carassius cuvieri × Carassius auratus red var. In fish, the biological function of PTXF is essentially unknown. For this purpose, we report the identification and analysis of WR-PTXF and elucidate its role in the antibacterial innate immunity. WR-PTXF contains 224 amino acids and shares 79.8% and 23.0% sequence identities with crucian carp CRP and SAP, respectively. Blast analysis shows that WR-PTXF and goldfish PTXF had the highest similarity (97.3%). WR-PTXF is expressed in multiple tissues and is upregulated by Aeromonas hydrophila infection. WR-PTXF contains a short pentraxin domain and recombinant WR-PTXF protein (rWR-PTXF) can bind the A. hydrophila in a concentration-dependent manner. Further, rWR-PTXF displays apparent bacteriostatic activity against A. hydrophila in vitro by enhancing the uptake of the bound bacteria by host phagocytes. When introduced in vivo, rWR-PTXF not only protects the gut mucosa but also limits the colonization of A. hydrophila in systemic immune organs. Consistently, knockdown of WR-PTXF significantly promotes bacterial dissemination in the tissues of host. These results indicate that WR-PTXF is a classic pattern recognition molecule that exerts a protective effect against bacterial infection.

Comparison of Growth Performance and Biochemical Components between Low-Salinity-Tolerant Hybrid and Normal Variety of Pacific White Shrimp (Penaeus vannamei)

Penaeus vannamei, a high-yield economical shrimp, is confronting germplasm degradation in the culture environments found in China, which results in a sharp drop in production. Genetic improvement by hybridization is an effective way to solve this problem. In this study, we selected the hybrid species adapted to low-salinity culture obtained by intraspecific crossing as the experimental group. The control group consisted of normal variety from the Hainan Lutai Company. The two groups of shrimps were cultured for three months under salinities of 1 PSU, 5 PSU, and 15 PSU. Growth-performance-related indicators, biochemical composition, and molting-related gene expression were examined. The results showed that at salinities of 1 PSU and 5 PSU, the survival rate and growth performance of the low-salt breeding group were better than those of the normal variety population. The digestive enzyme activity in the low-salt breeding group was higher, which was consistent with its better growth performance, and was also associated with higher triglyceride, total cholesterol, and glycogen content. Lower levels of lactic acid indicated less anaerobic metabolism and better adaptability to the environment. The amino acid and fatty acids analysis showed that levels of essential amino acids and high unsaturated fatty acids were both higher in the low-salt breeding group than in the normal variety shrimp cultured in a low-salinity environment. The expression levels of genes associated with molting (CHS, CaMKI, RXR, EcR, HSP60, and HSP70) were also higher in the low-salt breeding group than in the control group. The results indicated that the hybrid shrimp showed better growth performance and nutritional advantages compared with the normal shrimp under salinities of 1 PSU and 5 PSU. This research provides a valuable reference for subsequent genetic breeding and shrimp culture.

Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus

BACKGROUND

Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream, BSB, 2n = 48) and Culter alburnus (Topmouth culter, TC, 2n = 48) was achieved to establish hybrid lineages (BT and TB), which provide valuable materials for exploring the mechanisms of distant hybridization fertility. In this study, the gonadal tissue transcriptomes of BSB, TC, BT-F1, and TB-F1 were sequenced using Illumina high-throughput sequencing technology to analyze the reproductive characteristics of BT and TB.

RESULTS

Differential gene expression analysis showed that the differentially expressed genes in BT vs BSB and BT vs TC were mainly enriched in signaling pathways not directly associated with meiosis. While, the differentially expressed genes of TB vs BSB and TB vs TC were mainly enriched in pathways related to meiosis, and most of them were down-regulated, indicating that meiosis is suppressed in TB. Under-dominance (UD) genes were enriched in pathways related to meiosis and DNA repair in TB. Over-dominance (OD) genes were enriched in MAPK signaling pathway, expression level dominance-BSB (ELD-B) genes were enriched in pathways related to steroid hormone synthesis and expression level dominance-TC (ELD-T) genes were not significantly enriched in any pathway in both BT and TB.

CONCLUSIONS

These results suggest that meiotic progression may not be affected in BT, whereas it is clearly inhibited in TB. Offspring of M. amblycephala maternal parent may have better genomic compatibility and fertility. Our study provides important information on the molecular mechanisms of breaking reproductive isolation in distantly hybridized fertile lineages.

Mitotic defects lead to unreduced sperm formation in cdk1-/- mutants

Unreduced gametes, that are important for species evolution and agricultural development, are generally believed to be formed by meiotic defects. However, we found that male diploid loach (Misgurnus anguillicaudatus) could produce not only haploid sperms, but also unreduced sperms, after cyclin-dependent kinase 1 gene (cdk1, one of the most important kinases in regulating cell mitosis) deletion. Observations on synaptonemal complexes of spermatocyte in prophase of meiosis and spermatogonia suggested that the number of chromosomes in some spermatogonia of cdk1^-/- loach doubled, leading to unreduced diploid sperm production. Then, transcriptome analysis revealed aberrant expressions of some cell cycle-related genes (such as ppp1c and gadd45) in spermatogonia of cdk1^-/- loach relative to wild-type loach. An in vitro and in vivo experiment further validated that Cdk1 deletion in diploid loach resulted in mitotic defects, leading to unreduced diploid sperm formation. In addition, we found that cdk1^-/- zebrafish could also produce unreduced diploid sperms. This study provides important information on revealing the molecular mechanisms behind unreduced gamete formation through mitotic defects, and lays the foundation for a novel strategy for fish polyploidy creation by using cdk1 mutants to produce unreduced sperms, which can then be used to obtain polyploidy, proposed to benefit aquaculture.

Comparison of Antioxidant Capacity and Muscle Amino Acid and Fatty Acid Composition of Nervous and Calm Hu Sheep

This study determined the effect of temperament on antioxidant capacity and the relationship between antioxidant capacity and the contents of amino acids (AA) and fatty acids (FA) in muscle of Hu sheep. Organ and muscle samples of five calm and five nervous Hu sheep were collected to determine the antioxidant capacity and the contents of AA and FA in muscle tissue. The concentrations of malondialdehyde (MDA) and superoxide excretion enzyme (SOD) in muscle and intestinal tissue of calm Hu sheep were lower than those of nervous Hu sheep (p < 0.01), and the activity of glutathione peroxidase (GSH-Px) in liver of calm Hu sheep was significantly higher than that of nervous Hu sheep (p = 0.050). The content of AA of calm Hu sheep was higher than that of nervous Hu sheep, especially the content of reductive amino acids, which was significantly higher than that of nervous Hu sheep (p = 0.029). Fatty acid content of nervous Hu sheep was higher than that of calm type, and saturated fatty acid content was significantly higher than that of calm type (p = 0.001). The SOD content in muscle tissue was positively correlated with the contents of aspartic acid (Asp), alanine (Ala) and lysine (Lys). Catalase (CAT) activity was positively correlated with Ala content. There was a significant positive correlation between total antioxidants (T-AOC) and glutamate (Glu) (p < 0.05). MDA concentration was positively correlated with lauric acid (C12:0), triseconic acid (C13:0), myristic acid (C14:0) content (p < 0.01), and ginkgo acid (C15:0) content. The total antioxidants (T-AOC) was negatively correlated with stearic acid (C18:0) (p < 0.05). Our conclusion is that the antioxidant capacity of calm Hu sheep is superior to that of nervous Hu sheep, which may be due to the higher AA (especially reductive amino acids (Arg, Lys, Ala and Glu)) content in the muscle and the lower FA (especially SFA) content, which improve the antioxidant capacity of the organism and allow for further exploration of the mechanisms by which animal temperament affects antioxidant performance.

Proteomics-based molecular and functional characteristic profiling of muscle tissue in Triploid crucian carp

Triploid crucian carp (TCC) is a kind of artificially bred fish with huge economic value to China. It has several excellent characteristics, such as fast growth, strong disease resistance and delicious taste. However, as a regionally specific fish, the underlying molecular mechanisms of these characteristics are largely unknown. In this study, we performed quantitative proteomics on the muscle tissues of TCC and its parents, allotetraploid (♂), red crucian carp (♀) and common carp. Combined with multiple bioinformatic analysis, we found that the taste of TCC can be mainly attributed to umami amino acid-enriched proteins such as PURBA, PVALBI and ATP5F1B, and that its rapid growth can be mainly ascribed to the high expression and regulation of metabolism-related proteins such as NDUFS1, ENO1A and CS. These play significant roles in substrate and energy metabolism, as well as in bias transformation. Subsequently, we identified several proteins, including MDH1AA, GOT1 and DLAT, that may serve as potential regulators of innate immunity by regulating the biosynthesis and transformation of significant antibiotics and antimicrobial peptides. In conclusion, this study can serve as a significant reference for similar investigations and shed light on the molecular and biological functions of individual proteins in TCC muscle tissue.

Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂)

Simple Summary

The eyestalk is a key organ in crustaceans that produces neurohormones and regulates a range of physiological functions. Eyestalk displacement was discovered in some first-generation (F1) offspring of the novel interspecific hybrid crab (Scylla serrata ♀ × S. paramamosain ♂). To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, high-quality transcriptome was reconstructed using single-molecule real-time (SMRT) sequencing. A total of 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in hybrid crabs with displaced eyestalks (DH). The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant gene ontology (GO) terms were related to the cuticle or chitin. Overall, this study highlights the underlying genetic mechanisms of eyestalk displacement and provide useful knowledge for mud crab (Scylla spp.) crossbreeding.

Abstract

The lack of high-quality juvenile crabs is the greatest impediment to the growth of the mud crab (Scylla paramamosain) industry. To obtain high-quality hybrid offspring, a novel hybrid mud crab (S. serrata ♀ × S. paramamosain ♂) was successfully produced in our previous study. Meanwhile, an interesting phenomenon was discovered, that some first-generation (F1) hybrid offspring’s eyestalks were displaced during the crablet stage I. To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, both single-molecule real-time (SMRT) and Illumina RNA sequencing were implemented. Using a two-step collapsing strategy, three high-quality reconstructed transcriptomes were obtained from purebred mud crabs (S. paramamosain) with normal eyestalks (SPA), hybrid crabs with normal eyestalks (NH), and hybrid crabs with displaced eyestalks (DH). In total, 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in DH. The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant GO terms were related to the cuticle or chitin. Overall, high-quality reconstructed transcriptomes were obtained for the novel interspecific hybrid crab and provided valuable insights into the genetic mechanisms of eyestalk displacement in mud crab (Scylla spp.) crossbreeding.

An improved hybrid bream derived from a hybrid lineage of Megalobrama amblycephala (♀)×Culter alburnus (♂)

Distant hybridization is an important technique in fish genetic breeding. In this study, based on the establishment of an allodiploid fish lineage (BT, 2n=48, F₁-F₆) derived from distant hybridization between female Megalobrama amblycephala (BSB, 2n=48) and male Culter alburnus (TC, 2n=48), and the backcross progeny (BTB, 2n=48) derived by backcrossing female F₁ of BT to male BSB, an improved hybrid bream (BTBB, 2n=48) was obtained by backcrossing BTB (♀) to BSB (♂). Moreover, the morphological and genetic characteristics of BTBB individuals were investigated; BTBB was similar to BSB in appearance but had a higher body height than BSB. The study results regarding chromosome numbers and DNA content indicated that BTBB is a diploid hybrid fish. The 5S rDNA and Hox gene of BTBB were inherited from the original parents. Gonadal development in BTBB was normal. On the other hand, BTBB had a faster growth rate, higher muscle protein level, and lower muscle carbohydrate level than BSB. Hence, bisexual fertile BTBB is promoted and can be applied as a high-quality fish, and it can also be used as a new fish germplasm resource to develop high-quality fish further. Thus, this study is of great significance for fish genetic breeding.

A Novel Allotriploid Hybrid Derived From Female Goldfish × Male Bleeker's Yellow Tail

Hybridization is a traditional and effective strategy to alter the genotypes and phenotypes of the offspring, and distant hybridization is a useful strategy to generate polyploids in fish. In this study, goldfish (Carassius auratus, GF, 2n = 100) and Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT, 2n = 48), which belong to different subfamilies, were crossed with each other. The cross of female GF × male YT successfully obtained hybrid offspring (GFYT hybrids), while the cross of female YT × male GF was lethal, and all the fertilized eggs stopped developing before the neurula stage of embryogenesis. All GFYT hybrids possessed 124 chromosomes (3n = 124) with two sets from GF and one set from YT. The measurable and countable traits of GFYT hybrids were identified, and the genetic characteristics of 5S rDNA between GFYT hybrids and their parents were also revealed. There were, respectively, four and three different 5S rDNA types in GF (assigned as GF-Ⅰ∼Ⅳ) and YT (assigned as YT-Ⅰ∼Ⅲ), and GFYT hybrids specifically inherited YT-Ⅰ and YT-Ⅱ 5S rDNA types from YT and GF-Ⅲ and GF-Ⅳ from GF. In addition, there were only testis-like and fat-like gonads been found in GFYT hybrids. Interestingly, there were pyknotic and heteromorphous chromatin and invaginated cell membrane observed in the spermatids of testis-like gonads, but no mature sperm were found. Furthermore, TUNEL assays indicated that, compared with control, apparent apoptotic signals, which were mainly distributed around spermatid regions, were detected in the testis-like gonads, and the expression of apoptosis pathway-related genes including p53, bcl-2, bax, and caspase9 was significantly upregulated. Moreover, the expression of meiosis-related genes including spo11, dmc1, and rad51 showed an abnormally high expression, but mns1 and meig1, two key genes involved in the maturation of spermatid, were extremely downregulated. In brief, this is the first report of allotriploid via distant hybridization between GF and YT that possessing different chromosome numbers in vertebrates. The obtainment of GFYT hybrids not only harbors potential benefits and application in aquaculture but also further extends the understanding of the influence of hybridization and polyploidization on the genomic constitution of the hybrid offspring. Furthermore, they can be used as a model to test the origin and consequences of polyploidization and served as a proper resource to study the underlying mechanisms of spermatogenesis dysfunctions.

miR-199-5p regulates spermiogenesis at the posttranscriptional level via targeting Tekt1 in allotriploid crucian carp

BACKGROUND

Sperm abnormalities are one of the primary factors leading to male sterility, but their pathogenesis is still unclear. Although miRNAs are suggested to exert important roles in the regulation of spermatogenesis at both transcriptional and posttranscriptional levels, little is currently known regarding the regulation of sperm flagella assembly by microRNAs (miRNAs). The role of miRNAs in the development of sperm abnormalities in sterile triploid fish has not been studied.

RESULTS

In this study, we found that miR-199-5p was widely expressed in all detected tissues of different-ploidy crucian carp. As one of the testis-specific candidate markers, Tekt1 was predominantly expressed in the testis. Quantitative real-time PCR (qRT-PCR) analyses showed that the expression trend of miR-199-5p was exactly opposite to that of Tekt1. Through bioinformatics analysis, we identified a putative miR-199-5p binding site in the Tekt1 mRNA. We further identified Tekt1 as a target of miR-199-5p using luciferase reporter assay. Finally, we confirmed that miR-199-5p was necessary for sperm flagellar assembly and spermatogenesis in vivo via intraperitoneal injection of miR-199-5p antagomir or agomir in diploid red crucian carp. Moreover, miR-199-5p gain-of-function could lead to spermatids apoptosis and abnormal spermatozoa structure, which is similar to that of allotriploid crucian carp.

CONCLUSIONS

Our studies suggested that abnormally elevated miR-199-5p inhibited the sperm flagella formation in spermiogenesis by negatively regulating the expression of Tekt1, thereby causing sperm abnormalities of male allotriploid crucian carp.

Phylogeographic relationships and the evolutionary history of the Carassius auratus complex with a newly born homodiploid raw fish (2nNCRC)

Background

An important aspect of studying evolution is to understand how new species are formed and their uniqueness is maintained. Hybridization can lead to the formation of new species through reorganization of the adaptive system and significant changes in phenotype. Interestingly, eight stable strains of 2nNCRC derived from interspecies hybridization have been established in our laboratory. To examine the phylogeographical pattern of the widely distributed genus Carassius across Eurasia and investigate the possible homoploid hybrid origin of the Carassius auratus complex lineage in light of past climatic events, the mitochondrial genome (mtDNA) and one nuclear DNA were used to reconstruct the phylogenetic relationship between the C. auratus complex and 2nNCRC and to assess how demographic history, dispersal and barriers to gene flow have led to the current distribution of the C. auratus complex.

Results

As expected, 2nNCRC had a very close relationship with the C. auratus complex and similar morphological characteristics to those of the C. auratus complex, which is genetically distinct from the other three species of Carassius. The estimation of divergence time and ancestral state demonstrated that the C. auratus complex possibly originated from the Yangtze River basin in China. There were seven sublineages of the C. auratus complex across Eurasia and at least four mtDNA lineages endemic to particular geographical regions in China. The primary colonization route from China to Mongolia and the Far East (Russia) occurred during the Late Pliocene, and the diversification of other sublineages of the C. auratus complex specifically coincided with the interglacial stage during the Early and Mid-Pleistocene in China.

Conclusion

Our results support the origin of the C. auratus complex in China, and its wide distribution across Eurasia was mainly due to natural Pleistocene dispersal and recent anthropogenic translocation. The sympatric distribution of the ancestral area for both parents of 2nNCRC and the C. auratus complex, as well as the significant changes in the structure of pharyngeal teeth and morphological characteristics between 2nNCRC and its parents, imply that homoploid hybrid speciation (HHS) for C. auratus could likely have occurred in nature. The diversification pattern indicated an independent evolutionary history of the C. auratus complex, which was not separated from the most recent common ancestor of C. carassius or C. cuvieri. Considering that the paleoclimate oscillation and the development of an eastward-flowing drainage system during the Pliocene and Pleistocene in China provided an opportunity for hybridization between divergent lineages, the formation of 2nNCRC in our laboratory could be a good candidate for explaining the HHS of C. auratus in nature.

Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂)

Hybrid tilapia were produced from hybridization of Nile tilapia (Oreochromis niloticus) and blue tilapia (O. aureus). Comparative transcriptome analysis was carried out on the liver of hybrid tilapia and their parents by RNA sequencing. A total of 2319 differentially expressed genes (DEGs) were identified. Trend co-expression analysis showed that non-additive gene expression accounted for 67.1% of all DEGs. Gene Ontology and KEGG enrichment analyses classified the respective DEGs. Gene functional enrichment analysis indicated that most up-regulated genes, such as FASN, ACSL1, ACSL3, ACSL6, ACACA, ELOVL6, G6PD, ENO1, GATM, and ME3, were involved in metabolism, including fatty acid biosynthesis, unsaturated fatty acid biosynthesis, glycolysis, pentose phosphate pathway, amino acid metabolism, pyruvate metabolism, and the tricarboxylic acid cycle. The expression levels of a gene related to ribosomal biosynthesis in eukaryotes, GSH-Px, and those associated with heat shock proteins (HSPs), such as HSPA5 and HSP70, were significantly down-regulated compared with the parent tilapia lineages. The results revealed that the metabolic pathway in hybrid tilapia was up-regulated, with significantly improved fatty acid metabolism and carbon metabolism, whereas ribosome biosynthesis in eukaryotes and basal defense response were significantly down-regulated. These findings provide new insights into our understanding of growth heterosis in hybrid tilapia.

Identification and comparative study of melanoma differentiation-associated gene 5 homologues of triploid hybrid fish and its parents

Sterile triploid fish (3n = 150), derived from the hybridization between red crucian carp (Carassius auratus red var., ♀, 2n = 100) and allotetraploid (♂, 4n = 200), exhibits the improved disease resistance compared with its parents, but the current knowledge of the immunity of triploid fish is limited. Here, we report the identification and characterization of melanoma differentiation-associated gene 5 (MDA5) homologues from red crucian carp, triploid fish and allotetraploid. In this study, one red crucian carp MDA5 transcript (2nMDA5), two triploid fish MDA5 transcripts (3nMDA5-a and 3nMDA5-b) and two allotetraploid fish MDA5 transcripts (4nMDA5-a and 4nMDA5-b) have been cloned and identified separately. Immunofluorescence staining assay displayed that these MDA5 proteins were cytoplasmic proteins. RT-qPCR assay showed that, in response to spring viremia of carp virus (SVCV) and poly (I:C) stimuli, the increase of 3nMDA5 mRNA level was obviously higher than those of 2nMDA5 and 4nMDA5. Interestingly, the reporter assay and plaque assay revealed collectively that 3nMDA5-b, a shorter splicing form of MDA5, exhibited the strongest IFN promoter-inducing ability and antiviral activity. Additionally, when co-expressed with 3nMAVS, 3nMDA5-b induced a considerably higher level of IFN promoter activation than 3nMDA5-a; and the interactions between 3nMAVS/3nMDA5-a and 3nMAVS/3nMDA5-b were verified by co-IP assay. Taken together, our findings support the conclusion that in triploid fish, 3nMDA5-b mediates a robust antiviral signaling in host innate immune response.

First successful hybridization experiment between native European weatherfish (Misgurnus fossilis) and non-native Oriental weatherfish (M. anguillicaudatus) reveals no evidence for postzygotic barriers

The European weatherfish Misgurnus fossilis (Linnaeus, 1758) is a threatened freshwater species in large parts of Europe and might come under pressure from currently establishing exotic weatherfish species. Additional threats might arise if those species hybridize which has been questioned in previous research. Regarding the hybridization of M. fossilis × M. anguillicaudatus (Cantor, 1842), we demonstrate that despite the considerable genetic distance between parental species, the estimated long divergence time and different ploidy levels do not represent a postzygotic barrier for hybridization of the European and Oriental weatherfish. The paternal species can be easily differentiated based on external pigment patterns with hybrids showing intermediate patterns. No difference in standard metabolic rate, indicating a lack of hybrid vigour, renders predictions of potential threats to the European weatherfish from hybridization with the Oriental weatherfish difficult. Therefore, the genetic and physiological basis of invasiveness via hybridization remains elusive in Misgurnus species and requires further research. The existence of prezygotic reproductive isolation mechanisms and the fertility of F1 hybrids remains to be tested to predict the potential threats of globally invasive Oriental weatherfish species.

Transcriptome profiling revealed the growth superiority of hybrid pufferfish derived from Takifugu obscurus ♀ × Takifugu rubripes ♂

Hybridization is an efficient method to breed new strains of aquatic animals. In the present study, we produced a hybrid puffer by crossing female obscure puffer with male tiger puffer. The hybrid puffer could live in fresh water like obscure puffer and exhibited growth superiority. The averaged body weight of 4- and 6-month-old hybrid puffer were respectively 38.06% and 38.93% higher than that of obscure puffer. Then, we analyzed the underlying genetic basis for the growth advantage of hybrid puffer by comparative transcriptome analysis. A total number of 4264 and 1285 differentially expressed genes (DEGs) were respectively identified from pituitary and liver transcriptome profiles between hybrid puffer and obscure puffer. Comprehensive analysis showed that the DEGs related with cell proliferation and differentiation, and protein synthesis and export, specifically showed higher expression levels in hybrid puffer, such as "ECM-receptor interaction", "focal adhesion", "protein export" and "protein processing in endoplasmic reticulum". While the DEGs involved in gametogenesis and carbohydrate and energy metabolism highly expressed in obscure puffer, such as "oxidative phosphorylation", "citrate cycle", "progesterone-mediated oocyte maturation" and "oocyte meiosis". Furthermore, a series of candidate genes related to the growth superiority of hybrid puffer were identified, such as fn1a, ptprc, plcg2, igf1, tgfβ1, bmp4, abl1, col1a2, col1a1a, and myl9a. These results will be beneficial to understand the molecular basis of growth superiority and helpful to the hybrid breeding of pufferfish.

Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂)

Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF₁, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF₁, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF₁. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF₁ with significantly different expression levels.

A New Type of Allodiploid Hybrids Derived From Female Megalobrama amblycephala × Male Gobiocypris rarus

Distant hybridization can combine whole genomes from parent species and result in changes in the phenotypes and genotypes in hybrids. The characteristics of many hybrid fishes with even number of chromosomes have been reported, but the hybrids with odd number chromosomes are rarely reported. Blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48) and rare gudgeon (Gobiocypris rarus, RG, 2n = 50) belong to two different subfamilies and have quite different biological characteristics. In this study, we obtain the hybrids (BR) derived from the inter-subfamily hybridization of female BSB and male RG. We investigate the fertilization rate, hatching rate, morphological traits, chromosomal numbers, DNA content, growth rates, and 5S rDNA in the BR. The results show that the BR is an allodiploid fish with 49 chromosomes, and all the measurable traits are significantly different (p < 0.05) among BR, BSB, and BR. Interestingly, the upper part of the BR body color is similar to BSB (gray), the lower part of the BR body color is similar to RG (light yellow), and the BR inherits a unique light yellow wide longitudinal band from the RG. Furthermore, the BR has a fast growth rate compared with RG. The 5S rDNA of the BR inherits the specific bands of its parental 5S rDNA respectively and has some mutations, which show obvious recombination, heredity, and variability in BR. This study will be of great significance in fish genetic breeding.

Distant hybridization and gynogenesis between Nile tilapia Oreochromis niloticus and Jaguar cichlid Parachromis managuensis

To investigate the distant hybridization and gynogenesis between Nile tilapia Oreochromis niloticus and Jaguar cichlid Parachromis managuensis, reciprocal crossing was first performed between the two species. No offspring, however, were viable when there were these hybridizations. Gynogenesis was induced in O. niloticus and P. managuensis using ultraviolet (UV)-irradiated spermatozoa from P. managuensis and O. niloticus, respectively. The morphology during embryonic development indicated gynogenetic offspring of both O. niloticus and the P. managuensis were normal and deformed, and the results from flow cytometric analysis indicated normal fry were diploid and deformed fry were haploid. Gynogenetic O. niloticus and P. managuensis had the same DNA content and chromosome number as their species of origin, indicating that gynogenetic individuals were produced in both species. The presence of only females for both gynogenetic P. managuensis and O. niloticus was indicative of an XX genotype in the female P. managuensis and O. niloticus. Results from studies on genetic diversity indicated the average heterozygosity of the gynogenetic diploid population of O. niloticus were less than that of the cultured population, but the genetic homozygosity of the gynogenetic diploid population of O. niloticus was greater than that of the cultured population after one generation of gynogenesis, which achieved the goal of rapidly establishing genetic homozygosity.

CMPK2 of triploid crucian carp is involved in immune defense against bacterial infection

Cytidine/uridine monophosphate kinase 2 (CMPK2) is a thymidylate kinase and in mammals is known to be involved in mitochondrial DNA (mtDNA) synthesis and antiviral immunity. However, very little is known about the function of CMPK2 in fish. With an aim to elucidate the antimicrobial mechanism of CMPK2 in fish, we in this study examined the function of CMPK2 from triploid crucian carp (3nCmpk2). 3nCmpk2 is 426 residues in length and possesses the conserved thymidylate kinase domain. The deduced amino acid sequence of 3nCmpk2 shares 53.2%-99.1% overall identities with the CMPK2 of several fish species. Quantitative real time RT-PCR (qRT-PCR) analysis showed that 3nCmpk2 expression occurred in multiple tissues and was upregulated by bacterial infection in a time-dependent manner. Recombinant 3nCmpk2 (r3nCmpk2) induced mtDNA synthesis and NLRP3 activation. Overexpression of 3nCmpk2 protects the intestinal barrier and hampers the bacterial colonization in fish tissues. These results provide the first evidence that 3nCmpk2 is involved in host innate immunity and plays a protective role in antimicrobial responses during bacterial infection.

Comparative analyses of hypothalamus transcriptomes reveal fertility-, growth-, and immune-related genes and signal pathways in different ploidy cyprinid fish

Triploid crucian carp (TCC) is obtained by hybridization of female diploid red crucian carp (Carassius auratus red var., RCC) and male allotetraploid hybrids. In this study, high-throughput sequencing was used to conduct the transcriptome analysis of the female hypothalamus of diploid RCC, diploid common carp (Cyprinus carpio L., CC) and TCC. The key functional expression genes of the hypothalamus were obtained through functional gene annotation and differential gene expression screening. A total of 71.56 G data and 47,572 genes were obtained through sequencing and genome mapping, respectively. The Fuzzy Analysis Clustering assigned the differentially expressed genes (DEGs) into eight groups, two of which, overdominance expression (6005, 12.62%) and underdominance expression (3849, 8.09%) in TCC were further studied. KEGG enrichment analysis showed that the DEGs in overdominance were mainly enriched in four pathways. The expression of several fertility-related genes was lower levels in TCC, whereas the expression of several growth-related genes and immune-related genes was higher levels in TCC. Besides, 15 DEGs were verified by quantitative real-time PCR (qPCR). The present study can provide a reference for breeding sterility, fast-growth, and disease-resistant varieties by distant hybridization.

Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus

The Sox gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the Sox gene family in teleosts, the Sox genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, Megalobrama amblycephala, BSB), goldfish (2n = 100, Carassius auratus red var., 2nRCC), and autotetraploid C. auratus (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 Sox genes in zebrafish (2n = 50, Danio rerio), 26, 47, and 92 putative Sox genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of Sox genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of Sox genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the Sox gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the Sox gene family in polyploid vertebrates after several rounds of WGD events.

3nLcn2, a teleost lipocalin 2 that possesses antimicrobial activity and inhibits bacterial infection in triploid crucian carp

Lipocalin 2 (Lcn2) has been identified in mammals, however, the in vivo function of fish Lcn2 is essentially unknown. Triploid crucian carp (3n = 150) of red crucian carp (female, 2n = 100) and allotetraploid (male, 4n = 200) shows better resistance to pathogenic infections. To elucidate the antimicrobial mechanism of triploid crucian carp, we examined the function of a novel Lcn2 from triploid crucian carp (3nLcn2). 3nLcn2 is 183 residues in length and contains a conserved lipocalin domain. Quantitative real time reverse transcription PCR (qRT-PCR) analysis showed that 3nLcn2 expression occurred in multiple tissues and was upregulated by bacterial infection in a time-dependent manner. We found that purified recombinant 3nLcn2 (r3nLcn2) exerted bactericidal activity to Aeromonas hydrophila and Escherichia coli. qRT-PCR detected increased expression of pro-inflammatory cytokines and tight junctions in fish with 3nLcn2 overexpression. Fish administered with 3nLcn2 exhibited enhanced intestinal barrier and resistance against bacterial infection. These results provide the first evidence that 3nLcn2 is a functional lipocalin with antimicrobial activity and plays a positive role in the immune defense during bacterial infection.

Further evidence for paternal DNA transmission in gynogenetic grass carp

Gynogenesis is an important breeding method in aquaculture and has been widely applied to many fish species. If gynogenetic progenies are to inherit paternal partial genomic DNA, this will increase genetic variation and will provide a useful outcome for breeding. In this study, we investigated the genetic variation in homeobox (Hox) gene clusters (HoxA4a, HoxA9a, HoxA11b, HoxB1b, HoxC4a, HoxC6b, and HoxD10a) among koi carp (Cyprinus carpio haematopterus, KOC; the stimulation sperm source), grass carp (Ctenopharyngodon idellus), and gynogenetic grass carp (GGC). We found paternal DNA (a special DNA fragment and HoxC6b) derived from KOC and a recombinant gene belonging to HoxC6b in GGC. We are the first to report the recombinant HoxC6b in GGC. Our study provides further evidence for paternal DNA transmission to gynogenetic progenies, which is a finding with great significance for the genetic breeding of fish.

Effect of acclimated temperature on thermal tolerance, immune response and expression of HSP genes in Labeo rohita, Catla catla and their intergeneric hybrids

The ability of a species and population to respond to a decrease or an increase in temperature depends on their adaptive potential. Here, the critical thermal tolerance (CTmax and CTmin) of four populations: Labeo rohita, Catla catla, and their reciprocal hybrids L. rohita♀× C. catla♂ (RC) and C. catla♀ × L. rohita♂ (CR) being acclimatized at four acclimation temperatures (22, 26, 30 and 34 °C) were determined. All populations indicated substantial variations (P < 0.05) in CTmax and CTmin values. L. rohita displayed, comparatively the highest CTmax with largest total and intrinsic polygon zones as well as the upper and lower acquired thermal tolerance zones followed by RC and CR hybrids, while C. catla showed significantly the highest CTmin value and the smallest intrinsic and acquired thermal tolerance zones. Both hybrids illustrated low parent heterosis (≤11%). Additionally, the highest expression of Hsp70 and Hsp90 (heat shock proteins) genes, serum lysozyme level, respiratory burst activity and lowest lipid peroxidation level under lower and higher temperature shock further illustrated strong physiological mechanism of L. rohita in contrast to C. catla, to deal with acute temperature, while hybrids, especially F1 RC hybrid appeared as a good option to replace C. catla in relatively higher and lower temperature areas.

Comparative analyses of the Sox9a-Amh-Cyp19a1a regulatory Cascade in Autotetraploid fish and its diploid parent

BACKGROUND

Autotetraploid Carassius auratus (4nRCC, 4n = 200, RRRR) was derived from the whole genome duplication of diploid red crucian carp (Carassius auratus red var.) (2nRCC, 2n = 100, RR). To investigate the genetic effects of tetraploidization, we analyzed DNA variation, epigenetic modification and gene expression changes in the Sox9a-Amh-Cyp19a1a regulatory cascade between 4nRCC and 2nRCC.

RESULTS

We found that the Sox9a gene contained two variants in 2nRCC and four variants in 4nRCC. Compared with that in 2nRCC, DNA methylation in the promoter regions of the Amh and Cyp19a1a genes in 4nRCC was altered by single nucleotide polymorphism (SNP) mutations, which resulted in the insertions and deletions of CpG sites, and the methylation levels of the Sox9a, Amh and Cyp19a1a genes increased after tetraploidization. The gene expression level of the Sox9a-Amh-Cyp19a1a regulatory cascade was downregulated in 4nRCC compared with that in 2nRCC.

CONCLUSION

The above results demonstrate that tetraploidization leads to significant changes in the genome, epigenetic modification and gene expression in the Sox9a-Amh-Cyp19a1a regulatory cascade; these findings increase the extant knowledge regarding the effects of polyploidization.