Carassius auratus x Cyprinus carpio
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PROVIDER: PRJNA1103962 | ENA |
REPOSITORIES: ENA
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Project description:BACKGROUND:Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to answer whether the expression of reported traditional reference genes changes or not in the polyploid fish RESULTS: By retrieving the mRNA sequencing data of three different ploidy fish from the NCBI SRA database, we selected 12 candidate reference genes, and examined their expression levels in the 10 tissues and in the four cell lines of three different ploidy fish by real-time PCR. Then, the expression profiles of these 12 candidate reference genes were systematically evaluated by using the software platforms: BestKeeper, NormFinder and geNorm. CONCLUSION:The 28S ribosomal protein S5 gene (RPS5) and the ribosomal protein S18 gene (RPS18) are the most suitable reference genes for the polyploid of Cyprinus carpio and Carassius auratus, demonstrated by both of the tissues and the cultured cells.
| S-EPMC7499967 | biostudies-literature
Project description:Surrogate broodstock technology can increase the production efficiency of commercially important fishes that are difficult to breed in confinement and aid the propagation and recovery of endangered populations. In this study, we report the application of germ cell (GC) transplantation (GCT) for increasing the numbers of progeny produced by small-bodied ornamental fishes by using sexually mature adult fish as recipients. The GCs isolated from prepubertal male goldfish (Carassius auratus) donors (n = 5) were transplanted through the genital papilla into the gonads of adult common carp (Cyprinus carpio) recipients. The endogenous GCs of the recipient were depleted using busulfan (40 mg/kg body weight [BW]; in five doses at 2-week intervals) and high-temperature (38 °C) treatments. Within 4 months after GCT, the donor GCs recolonised the recipients' gonads and resumed gametogenesis. The presence of donor-derived gametes was confirmed through polymerase chain reaction-restriction fragment length polymorphism analysis in all the surrogate common carp males and females. Artificial fertilisation and induced spawning between surrogate males and females yielded pure goldfish progeny; the fertilisation and hatching rates were similar to those of the controls. These results suggest that GCT could also be potentially applied in commercial aquaculture, mainly to increase the numbers of progeny obtained from small-bodied fishes those having low gamete counts.
| S-EPMC9794659 | biostudies-literature
Project description:Carassius auratus x Cyprinus carpio Transcriptome or Gene expression
| PRJNA86641 | ENA
Project description:Carassius auratus x Cyprinus carpio Transcriptome or Gene expression
| PRJNA260655 | ENA
Project description:Carassius auratus x Cyprinus carpio overview
| PRJNA86729 | ENA
Project description:Rediploidization is considered to be a part of the evolutionary history of allotetraploids, and resulted in the emergence of novel epigenetic regulatory activities. To study the changing patterns of gene expression following the reduction of a genome by 50%, we used RNA-seq and quantitative real-time PCR (qPCR) to investigate total gene expression and homoeolog expression in three hybrids of a C. auratus red var. (2n = 100, ♀) (R) and C. carpio (2n = 100, ♂) (C) (i.e., F1, F18, and G4) and their original parents. A comparison of homoeolog expression between G4 and F18 identified 7 genes (0.22%) that exhibited novel R/C homoeolog expression patterns in G4, while 4 genes (0.12%) were affected by R/C homoeolog silencing. We determined the direction and extent of the homoeolog expression bias (HEB). The C-HEB genes (i.e., nrp1a and igf1) and R-HEB genes (i.e., fgf23 and esm1) provided insights into the effects of the dominance of one parental homoeolog expression on growth regulation. This dominance may contribute to the rapid growth of G4 fish. Our findings may be relevant for clarifying the relationship between growth heterosis and differences in homoeolog expression patterns.
| S-EPMC5651915 | biostudies-literature
Project description:Hybridization and polyploidization may lead to divergence in adaptation and boost speciation in angiosperms and some lower animals. Epigenetic change plays a significant role in the formation and adaptation of polyploidy. Studies of the effects of methylation on genomic recombination and gene expression in allopolyploid plants have achieved good progress. However, relevant advances in polyploid animals have been relatively slower. In the present study, we used the bisexual, fertile, genetically stable allotetraploid generated by hybridization of Carassius auratus red var. and Cyprinus carpio L. to investigate cytosine methylation level using methylation-sensitive amplification polymorphism (MSAP) analysis. We observed 38.31% of the methylation changes in the allotetraploid compared with the parents at 355 randomly selected CCGG sites. In terms of methylation status, these results indicate that the level of methylation modification in the allotetraploid may have increased relative to that in the parents. We also found that the major methylation changes were hypermethylation on some genomic fragments and genes related to metabolism or cell cycle regulation. These results provide circumstantial evidence that DNA methylation might be related to the gene expression and phenotype variation in allotetraploid hybrids. Our study partly fulfils the need for epigenetic research in polyploid animals, and provides evidence for the epigenetic regulation of allopolyploids.
| S-EPMC3574156 | biostudies-literature
Project description:Cyprinid herpesvirus-3 (CyHV-3, syn. koi herpesvirus) is an important pathogen worldwide and a common cause of mass mortality events of wild common carp (Cyprinus carpio) in North America, however, reference strains and genomes obtained from wild carp are not available. Additionally, it is unclear if fishes in North America are susceptible to CyHV-3 infection due to incomplete susceptibility testing. Here we present the first North American type strain and whole-genome sequence of CyHV-3 isolated from wild carp collected from a lake with a history and recent incidence of carp mortality. Additionally, the strain was used in an in-vivo infection model to test the susceptibility of a common native minnow (Pimephales promelas) and goldfish (Carrasius auratus) which is invasive in North America. Detection of CyHV-3 DNA was confirmed in the tissues of a single fathead minnow but the same tissues were negative for CyHV-3 mRNA and samples from exposed fathead minnows were negative on cell culture. There was no detection of CyHV-3 DNA or mRNA in goldfish throughout the experiment. CyHV-3 DNA in carp tissues was reproducibly accompanied by the detection of CyHV-3 mRNA and isolation on cell culture. Additionally, environmental CyHV-3 DNA was detected on all tank filters during the study. These findings suggest that fathead minnows and goldfish are not susceptible to CyHV-3 infection and that detection of CyHV-3 DNA alone in host susceptibility trials should be interpreted with caution.
| S-EPMC7820613 | biostudies-literature
Project description:BACKGROUND:Hox transcription factors are master regulators of animal development. Although highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generation of hybrid species, thus potentially serving as species-specific molecular markers. Here, we systematically studied the evolution of genomic sequences of Hox loci in an artificial allotetraploid lineage (4nAT, 4n?=?200) derived from a red crucian carp (?, RCC, 2n?=?100)?×?common carp (?, CC, 2n?=?100) cross and its parents (RCC and CC). RESULTS:PCR amplification yielded 23 distinct Hox gene fragments from 160 clones in 4nAT, 22 fragments from 90 clones in RCC, and 19 fragments from 90 clones in CC. Sequence alignment of the HoxA3a and HoxC10a genes indicated both the inheritance and loss of paternal genomic DNA in 4nAT. The HoxA5a gene from 4nAT consisted of two subtypes from RCC and two subtypes from CC, indicating that homologous recombination occurred in the 4nAT hybrid genome. Moreover, 4nAT carried genomic pseudogenization in the HoxA10b and HoxC13a loci. Interestingly, a new type of HoxC9a gene was found in 4nAT as a hybrid sequence of CC and RCC by recombination in the intronic region. CONCLUSION:The results revealed the influence of Hox genes during polyploidization in hybrid fish. The data provided insight into the evolution of vertebrate genomes and might be benefit for artificial breeding programs.
| S-EPMC7057633 | biostudies-literature
Project description:Cyprinus carpio wuyuanensis x Carrassius auratus overview
| PRJNA168531 | ENA