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Procedure for generating the reciprocal cross hybrids of BSB and TC. (A) BSB. (B) TC. (C ) BTF 1 of BSB (♀) × TC (♂). (D) BTF 2 produced by intercrossing within BTF 1 . (E) BTF 3 obtained by intercrossing within BTF 2 . (F ) TBF 1 of TC (♀) × BSB (♂). (G) BTF 2 produced by intercrossing within TBF 1 . (H) TBF 3 obtained by intercrossing within TBF 2 . The images of the fish hybrids are only representative of certain progeny. (Scale bar) 3 cm.
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Hybridization can combine the genomes of different strains or species, which leads to changes of genotype and phenotype in the hybrids. In this study, we aimed to investigate the genetic variations of hybrids (WR-F1 and WR-F2) derived from the intraspecific hybridization of white crucian carp (Carassius auratus cuvieri, WCC, ♀) and red crucian carp...
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... [TC]; 2n = 48), which reached sexual maturity in natural waters of the Yangtze River in China, were collected for the hybrid experiments. The procedure for generating the hybrid lineages investigated in this study is shown in Figure 1. BSB and TC were used as the parents in the reciprocal cross hybrids to form two types of hybrid lineages. ...
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... generated ∼192.54 Gb (180. Tables S1, S2; Supplemental Methods). The resulting assemblies were 1.09 Gb (BSB) and 1.02 Gb (TC) ( Table 1). These sizes were very similar to the genome sizes estimated through k-mer analysis and flow cytometry measures (Supplemental Fig. S1; Supplemental Methods). The lengths of contig N50/scaffold N50 were 142.73 kb/ 1.40 Mb and 72.24 kb/3.67 Mb for BSB and TC, respectively (Table 1). Assessments of genome assembly quality showed that the assemblies covered 99.50%/98.12% unigenes (41,825/41,614 for the BSB; 151,448/148,604 for the TC) derived from RNA-seq across multiple ...
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... 3 , and eight were shared in BTF 1 -BTF 3 (Supplemental Fig. S28). (Fig. 4A). Fig. S30). The similar phenomenon was detected in the liver tissues based on potential genes of BSB/TC allelic expression bias (Supplemental Table S18). However, the clear BSB allelic expression bias gradually weakened from F 1 to F 3 in both BT and TB (Supplemental Fig. S31). In addition, a similar number of BSB and TC allelic expression-biased genes (215 vs. 235 in the muscle of BTF 3 ; 162 vs. 168 in the gonad of BTF 3 ; TB: 185 vs. 202 in the muscle of TBF 3 ; 182 vs. 156 in the gonad of TBF 3 ) were observed (Supplemental Fig. ...
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... investigate allelic expression changes under parental effects, the log 2 (TC/BSB) values in parents were calculated and compared with the log 2 (TC/BSB) values of the hybrid offspring (Supplemental Methods). The results revealed a gradual decrease of the magnitude of allelic expression across three generations of hybrid progenies (P < 0.01) (Fig. 4B,C; Supplemental Fig. S31). Among the 9753 orthologous gene pairs in the parents, 1373 (14.07%) DEGs were observed between two parents in which only 440 (4.52%) and 586 (6.02%) DEGs between two alleles were found in BTF 1 and TBF 1 , respectively. Then, fewer DEGs were found in the next generations (4.40% in TBF 2 , 3.48% in TBF 3 , 4.22% in BTF 2 , and 3.04% ...
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... were observed between two parents in which only 440 (4.52%) and 586 (6.02%) DEGs between two alleles were found in BTF 1 and TBF 1 , respectively. Then, fewer DEGs were found in the next generations (4.40% in TBF 2 , 3.48% in TBF 3 , 4.22% in BTF 2 , and 3.04% in BTF 3 ) (Supplemental Fig. S31). Furthermore, a gradual decrease in "cis + trans," "cis only," and "conserved" genes (31.46%-18.37% in BTF 1 to BTF 3 ; 29.37%-17.04% in TBF 1 to TBF 3 ) showed the gradual weakening of the parental effect from F 1 to F 3 (Supplemental Table S19). ...
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... genetic relationship between the BSB and the TC in the family Cyprinidae ( Fig. 1A-H; Supplemental Fig. S3). These results laid good foundations for exploring the interspecific compatibility in their reciprocal cross hybrids. Different degrees of trait divergence in the two BSB/TC hybrid lineages provide enough samples to investigate potential mechanisms underlying these phenomena ( Fig. 6A,B; Supplemental Tables S21, S22; Xiao et al. ...
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... inheritance (Supplemental Table S19; Emerson et al. 2010;McManus et al. 2010). A similar phenomenon was observed in natural allopolyploid wheat (Feldman et al. 2012) and cotton ( Yoo et al. 2013). In addition, decreased and increased trends of gene expression at global and allelic levels were observed from F 1 to F 3 of the two hybrid lineages (Figs. 3, 4A; Supplemental Fig. S31). The direction and magnitude of gene expression changes in hybrids showed asymmetric patterns, which were often regulated by DNA methylation ( Wang et al. 2016;Choi et al. 2018), histone modification ( Schotanus et al. 2015), and microRNAs (Ambros ...
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... sperm of C. carpio haematopterus were obtained for whole-genome sequencing ( Gong et al. 2019). Then, 24 fish (age 2 yr), including three male TCs with mature testes, three BSBs with mature ovaries, three female individuals each from BTF 1 -BTF 3, and three female individuals each from TBF 1 -TBF 3 , were used in the subsequent analyses (Fig. 1A-H). The detailed descriptions about the sample preparation for genome and transcriptome sequencing were presented in the Supplemental ...
Citations
... As an introduced variety of crucian carp, JCC can be cultured in China on a large scale based on its growth advantages and adaptability. At present, JCC can not only be directly used for commercial production but also for hybridization with tetraploid fish or red crucian carp to produce the sterile triploid fish "XiangYun" crucian carp, "XiangYun" crucian carp No.2, "Hefang" crucian carp and "Hefang" crucian carp No. 2 (Liu et al., 2001;Liu et al., 2019;Liu et al., 2018). However, limited by the scale of introduction of the species and the mating of close relatives under the conditions of long-term artificial aquaculture, JCC is facing bottleneck problems such as insufficient quality resources and frequent diseases. ...
... According to previous studies, diploid hybrid fish (WR) was generated by crossing white crucian carp (Carassius cuvieri, WCC, ♀) and red crucian carp (Carassius auratus red var, RCC, ♂) (Liu et al., 2018;Wang et al., 2015). RCCs, WCCs and WRs were obtained from an aquaculture base in Wang Cheng district (Changsha, Hunan province, China). ...
Ferritin H can participate in the regulation of fish immunity. Tissue-specific analysis revealed that the highest expressions of Ferritin H in parental species were observed in spleen, while peaked level of Ferritin H mRNA in hybrid fish was observed in liver. In addition, A. hydrophila challenge could sharply enhance their Ferritin H mRNA expression in liver, kidney and spleen. To further investigate their roles in immune regulation, their Ferritin H fusion proteins were produced in vitro. Ferritin H fusion proteins could exhibit a direct binding activity to A. hydrophila and endotoxin in a dose-dependent manner, restrict dissemination of A. hydrophila to tissues and abrogate inflammatory cascades. Moreover, treatment with Ferritin H fusion proteins could reduce A. hydrophila-induced lipid peroxidation. These results indicated that Ferritin H in hybrid fish elicited a similar immune regulation of A. hydrophila-induced inflammatory signals in comparison with those of its parents.
... Distant hybridization is an important technique and widely used in fish genetic breeding, which can combine whole genomes from parent species and lead to changes in both phenotypes and genotypes in the offspring (Liu, 2010;Zhang et al., 2014;Xu et al., 2015a). For example, in terms of phenotypes, the allodiploid lineage with hybrid traits, high survival rate, good meat quality, and strong stress resistance were established by the distant hybridization of Japanese white crucian carp (Carassius cuvieri, ♀) and red crucian carp (Carassius auratus red var., ♂) (Wang et al., 2015;Liu et al., 2017Liu et al., , 2018Liu et al., , 2019a; the triploid fish with fast growth were produced by the crossing of diploid fish with allotetraploid fish (Tiwary et al., 2004;Zhong et al., 2012;Wang et al., 2020); in terms of genotypes, a high proportion of chimeric genes (>9%) have been found among orthologous genes in the transcriptomes of allotetraploid fish (Liu et al., 2016); many different expressed genes associated with sperm flagellar assembly and motility were found in testis transcriptomes from diploid fish and triploid fish (Xu et al., 2015b;Li et al., 2018a). These phenotypes and genotypes are very important for breeding applications and scientific research. ...
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.
... Hybrid fish (WR) were generated by crossing white crucian carp (Carassius cuvieri, WCC, ♀) and red crucian carp (Carassius auratus red var, RCC, ♂) [34]. RCCs, WCCs and WRs (average length 13.2 ± 0.52 cm) were obtained from an aquaculture base in Wang Cheng district (Changsha, China), which were acclimatized for two weeks and fed with commercial diet twice daily till 24 h before challenge experiment, respectively. ...
NK-lysin, an effector of natural killer (NK) cells and cytotoxic T lymphocytes (CTLs), not only exhibits cytotoxic effect in fish cells, but also participates in the immune defense against pathogenic infection. In this study, ORF sequences of RCC-NK-lysin, WCC-NK-lysin and WR-NK-lysin were 369 bp. Tissue-specific analysis revealed that the highest expressions of RCC-NK-lysin and WCC-NK-lysin were observed in gill, while the peaked level of WR-NK-lysin mRNA was observed in spleen. A. hydrophila infection sharply increased RCC-NK-lysin, WCC-NK-lysin and WR-NK-lysin mRNA expression in liver, trunk kidney and spleen. In addition, elevated levels of NK-lysin mRNA were observed in cultured fin cell lines of red crucian carp (RCC), white crucian carp (WCC) and their hybrid offspring (WR) after Lipopolysaccharide (LPS) challenge. RCC-NK-lysin, WCC-NK-lysin and WR-NK-lysin exerted regulatory roles in inducing ROS generation, modulating mitochondrial membrane potential, decreasing fish cell viability and antagonizing survival signalings, respectively. RCC/WCC/WR-NK-lysin-overexpressing fish could up-regulate expressions of inflammatory cytokines and decrease bacterial loads in spleen. These results indicated that NK-lysin in hybrid fish contained close sequence similarity to those of its parents, possessing the capacities of cytotoxicity and immune defense against bacterial infection.
... Because of their extensive morphological diversity and genetic background of allotetraploidy, goldfish make an excellent model for research in evolutionary developmental biology (Gui and Zhou, 2010;Ota and Abe, 2016;Zhou and Gui, 2017;Liu et al., 2018). They are also employed as model organisms in comparative endocrinology studies, especially in neuroendocrinology (Popesku et al., 2008;Blanco et al., 2018). ...
Goldfish comprise around 300 different strains with drastically altered and aesthetical morphologies making them suitable models for evolutionary developmental biology. The dragon-eye strain is characterized by protruding eyes (analogous to those of Chinese dragons). Although the strain has been selected for about 400 years, the mechanism of its eye development remains unclear. In this study, a stable dragon-eye goldfish strain with a clear genetic background was rapidly established and studied. We found that upregulation of the PPAR signaling pathway accompanied by an increase in lipid accumulation might trigger the morphological and structural transformation of the eye in dragon-eye goldfish. At the developmental stage of proptosis (eye protrusion), downregulation of the phototransduction pathway was consistent with the structural defects and myopia of the dragon-eye strain. With the impairment of retinal development, cytokine-induced inflammation was activated, especially after proptosis, similar to the pathologic symptoms of many human ocular diseases. In addition, differentially expressed transcription factors were significantly enriched in the PAX and homeobox families, two well-known transcription factor families involved in eye development. Therefore, our findings reveal the dynamic changes in key pathways during eye development in dragon-eye goldfish, and provide insights into the molecular mechanisms underlying drastically altered eyes in goldfish and human ocular disease.
... Similarly, we found that 19.04% of the chimeric genes were present in the distant hybrids of white crucian carp (WCC) and RCC, and these chimeric genes were significantly associated with the dominant traits of the hybrids. The hybrids had the characteristics of fast growth, strong resistance, and being rich in amino acids (Liu et al., 2018). The GF-L was the offspring of selfmating RCC-L. ...
Distant hybridization leads to obvious changes in genotypes and phenotypes, giving rise to species with novel capabilities. However, the fusion of distinct genomes also polymerizes the DNA or gene variations that occur during the course of evolution. Knowledge of the early stages of post-hybridization evolution is particularly important. Here, we investigated the full-length (FL) transcriptomes and the sequences resulting from the genome resequencing of the red crucian carp-like homodiploid fish (RCC-L) and goldfish-like homodiploid fish (GF-L) derived from the interspecific hybridization of koi carp (KOC) and blunt snout bream (BSB) to provide molecular evidence for the hybrid origin of the goldfish (GF). We compared the orthologous genes in the transcriptomes of RCC-L and GF-L with those of KOC and BSB. We also mapped the orthologous genes to the common carp (CC) and BSB genomes and classified them into eight gene patterns in three categories (chimaera, mutant, and biparental origin genes). The results showed that 48.20% and 46.50% of the genes were chimaera and that 3.70% and 8.30% of the genes were mutations of orthologous genes in RCC-L and GF-L, respectively. In RCC-L and GF-L, 63.70% and 68.20% of the genetic materials were from KOC, and 12.30% and 11.90% of the genetic materials were from BSB. The sequences from the genome resequencing of RCC-L and GF-L were mapped to the genome sequences of CC and BSB, revealing that the similarities of both RCC-L and GF-L to the CC genome (92.52%, 90.18%) were obviously higher than to the BSB genome (50.33%, 49.18%), supporting the suggestion that the genomes of both RCC-L and GF-L were mainly inherited from KOC but had some DNA fragments from BSB. Overall, our results provide molecular biological evidence for the hybrid origin of red crucian carp (RCC) and GF.
... Compared to distant hybridization, intraspecific hybridization triggers limited genetic variation, whereas it can generate hybrid offsprings harboring the excellent traits derived from their parents and establish a steady lineage [20]. Although several chimeric genes are observed and validated in hybrids by intraspecific hybridization [21], the data on the immune-related genetic variants of pro-inflammatory cytokines or MyD88-IRAK4 signaling and immunoregulatory function of chimeric hepcidin in hybrids are sparse. ...
... Hybrid crucian carp (WR), novel diploid hybrid fish (2n = 100), are generated by crossing white crucian carp (Carassius auratus cuvieri, WCC, ♀) with red crucian carp (Carassius auratus red var, RCC, ♂), which belong to Cypriniformes, Cyprinidae (genus Carassius) [20,21]. Additionally, crucian carp is also one of the most important economic fish in China. ...
... According to previous studies, diploid hybrid fish (WR) was generated by crossing white crucian carp (Carassius auratus cuvieri, WCC, ♀) and red crucian carp (Carassius auratus red var, RCC, ♂) [20,21]. ...
Hepcidin, a multifunctional hormone oligopeptide, not only exhibits a regulatory role in iron metabolism, but also participates in the regulation of teleostean immunity. In this study, ORF sequence of WR-hepcidin was 258 bp and encoded 85 amino acid residues. Tissue-specific analysis revealed that the highest expression of WR-hepcidin was observed in liver. Aeromonas hydrophila challenge can sharply increased WR-hepcidin mRNA expression in liver, trunk kidney and spleen. The purified WR-hepcidin fusion peptide can directly bind to A. hydrophila and Streptococcus agalactiae, reduce the relative bacterial activity, limit bacterial growth and attenuate their dissemination to tissues in vivo. In addition, the treatment of WR-hepcidin fusion protein can diminish the production of pro-inflammatory cytokines. These results indicated that WR-hepcidin can play a negative regulatory role in bacteria-stimulated pro-inflammatory cytokines production and MyD88-IRAK4 activation.
... and mutation events (1.02-1.16%) occurred in different generations of this nascent allopolyploids [17]; Liu et al. revealed 19.04%, 4.17% chimeric genes and 6.90%, 5.05% mutations of orthologous genes in F 1 and F 2 of diploid hybrids, respectively [18]. Distant hybridization can generate changes in phenotypes and genotypes, leading to the formation of new hybrid lineages with genetic variation and providing a good experimental model for tracing the changes of genetic and epigenetic levels in the early stage of distant hybridization. ...
Background:
Distant hybridization can generate changes in phenotypes and genotypes that lead to the formation of new hybrid lineages with genetic variation. In this study, the establishment of two bisexual fertile carp lineages, including the improved diploid common carp (IDC) lineage and the improved diploid scattered mirror carp (IDMC) lineage, from the interspecific hybridization of common carp (Cyprinus carpio, 2n = 100) (♀) × blunt snout bream (Megalobrama amblycephala, 2n = 48) (♂), provided a good platform to investigate the genetic relationship between the parents and their hybrid progenies.
Result:
In this study, we investigated the genetic variation of 12 Hox genes in the two types of improved carp lineages derived from common carp (♀) × blunt snout bream (♂). Hox gene clusters were abundant in the first generation of IDC, but most were not stably inherited in the second generation. In contrast, we did not find obvious mutations in Hox genes in the first generation of IDMC, and almost all the Hox gene clusters were stably inherited from the first generation to the second generation of IDMC. Interestingly, we found obvious recombinant clusters of Hox genes in both improved carp lineages, and partially recombinant clusters of Hox genes were stably inherited from the first generation to the second generation in both types of improved carp lineages. On the other hand, some Hox genes were gradually becoming pseudogenes, and some genes were completely pseudogenised in IDC or IDMC.
Conclusions:
Our results provided important evidence that distant hybridization produces rapid genomic DNA changes that may or may not be stably inherited, providing novel insights into the function of hybridization in the establishment of improved lineages used as new fish resources for aquaculture.
... The allelic recombination in somatic cells was also reported in Nicotiana tabacum ( Lebel et al. 1993), in F 1 hybrids of Carassius auratus cuvieri (♀) × C. auratus red var. (♂) ( Liu et al. 2018), and in F 1 hybrids of C. auratus red var. (♀) × Cyprinus carpio L. (♂) ( Liu et al. 2016). ...
Hybridization drives rapid speciation by shaping novel genotypic and phenotypic profiles. Genomic incompatibility and transcriptome shock have been observed in hybrids, although this is rarer in animals than in plants. Using the newly sequenced genomes of the blunt snout bream (Megalobrama amblycephala [BSB]) and the topmouth culter (Culter alburnus [TC]), we focused on the sequence variation and gene expression changes in the reciprocal intergeneric hybrid lineages (F1-F3) of BSB × TC. A genome-wide transcriptional analysis identified 145-974 expressed recombinant genes in the successive generations of hybrid fish, suggesting the rapid emergence of allelic variation following hybridization. Some gradual changes of gene expression with additive and dominance effects and various cis and trans regulations were observed from F1 to F3 in the two hybrid lineages. These asymmetric patterns of gene expression represent the alternative strategies for counteracting deleterious effects of the subgenomes and improving adaptability of novel hybrids. Furthermore, we identified positive selection and additive expression patterns in transforming growth factor, beta 1b (tgfb1b), which may account for the morphological variations of the pharyngeal jaw in the two hybrid lineages. Our current findings provide insights into the evolution of vertebrate genomes immediately following hybridization.
... Polyploidy is viewed as an important factor in eukaryote evolution [1][2][3]. Distant hybridization is a useful tool to produce hybrid offspring with altered genotypes and phenotypes or with different ploidy levels [4][5][6]. Fertile triploidy, as a special polyploidy population and a bridge to the formation of tetraploid populations, might play an important role in speciation [7,8]. In previous studies, arti cial autotriploid gynogenetic offspring (3n=150, AAA; abbreviated as 3nG) derived from Carassius auratus red var. ...
Background Polyploidization can induces a flurry of genetic events and plays an important role in speciation. In this study, we comparatively analyzed the molecular organization and chromosomal locus of 5S rDNA in natural autotriploid (3nCC, 3n=150) and artificial autotriploid gynogenetic (3nG, 3n=150) Carassius auratus as well as the related diploid ancestors, diploid Carassius auratus (2nCC, 2n=100) and Carassius auratus red var. (RCC, 2n=100), which provide a excellent model to ascertain the genomic changes in autotriploidization process. Results The similarities of the 5S rDNA coding region (class I, class II and class III) between RCC and 3nG were 98.3%, 100% and 99.1%, respectively, and the similarities of the 5S rDNA coding region (class IV, class V and class VI) between 2nCC and 3nCC were 97.5%, 100% and 100%, respectively. Fluorescence in situ hybridization (FISH) with 5S rDNA as probe indicated that the expected numbers of maternal chromosomal loci were found in 3nG and 3nCC, respectively. Conclusions These observations indicate that autotriploidization has little influence on the divergence of 5S rDNA family in Carassius auratus.
