Upregulation of the PPAR signaling pathway and accumulation of lipids are related to the morphological and structural transformation of the dragon-eye goldfish eye

Yu, Peng; Wang, Yan; Yang, Wentao; Li, Zhi; Zhang, Xiaojuan; Zhou, Li; Gui, Jian‐Fang

doi:10.1007/s11427-020-1814-1

Cited by 33 publications

(15 citation statements)

References 84 publications

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“…Viperin was sharply upregulated among three clones at post infection ( 52 ). Additionally, gibel carp has over 150 chromosomes and is considered an auto-allo-hexaploid in comparison with goldfish ( Carassius auratus ) with 100 chromosomes ( 53 , 54 ). It had been speculated that two rounds (2R) of polyploidy events, an allotetraploidy and an autotriploidy, occurred during its evolution ( 55 ).…”

Section: Introductionmentioning

confidence: 99%

Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish

Mou

et al. 2021

Front. Immunol.

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Polyploidy and subsequent diploidization provide genomic opportunities for evolutionary innovations and adaptation. The researches on duplicated gene evolutionary fates in recurrent polyploids have seriously lagged behind that in paleopolyploids with diploidized genomes. Moreover, the antiviral mechanisms of Viperin remain largely unclear in fish. Here, we elaborate the distinct antiviral mechanisms of two viperin homeologs (Cgviperin-A and Cgviperin-B) in auto-allo-hexaploid gibel carp (Carassius gibelio). First, Cgviperin-A and Cgviperin-B showed differential and biased expression patterns in gibel carp adult tissues. Subsequently, using co-immunoprecipitation (Co-IP) screening analysis, both CgViperin-A and CgViperin-B were found to interact with crucian carp (C. auratus) herpesvirus (CaHV) open reading frame 46 right (ORF46R) protein, a negative herpesvirus regulator of host interferon (IFN) production, and to promote the proteasomal degradation of ORF46R via decreasing K63-linked ubiquitination. Additionally, CgViperin-B also mediated ORF46R degradation through autophagosome pathway, which was absent in CgViperin-A. Moreover, we found that the N-terminal α-helix domain was necessary for the localization of CgViperin-A and CgViperin-B at the endoplasmic reticulum (ER), and the C-terminal domain of CgViperin-A and CgViperin-B was indispensable for the interaction with degradation of ORF46R. Therefore, the current findings clarify the divergent antiviral mechanisms of the duplicated viperin homeologs in a recurrent polyploid fish, which will shed light on the evolution of teleost duplicated genes.

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Section: Introductionmentioning

confidence: 99%

Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish

Mou

et al. 2021

Front. Immunol.

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“…Moreover, nine RNA samples of genotypic female gonads and nine RNA samples of genotypic male gonads at 18,22,26,30,35,40,47,58, and 70 dah were sequenced respectively via Illumina Hiseq platform at BGI-shenzhen, China (S8 Table ). Illumina clean reads were mapped to PacBio full-length transcriptome, and Fragments per Kilobase Million (FPKM) was used to quantify gene expression, which was calculated via RSEM (Version 1.2.12) [67,68]. To normalize gene expression, if the FPKM was 0, it would be modified to 0.001.…”

Section: Plos Geneticsmentioning

confidence: 99%

Genomic anatomy of male-specific microchromosomes in a gynogenetic fish

Ding

Zhu

et al. 2021

PLoS Genet

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Unisexual taxa are commonly considered short-lived as the absence of meiotic recombination is supposed to accumulate deleterious mutations and hinder the creation of genetic diversity. However, the gynogenetic gibel carp (Carassius gibelio) with high genetic diversity and wide ecological distribution has outlived its predicted extinction time of a strict unisexual reproduction population. Unlike other unisexual vertebrates, males associated with supernumerary microchromosomes have been observed in gibel carp, which provides a unique system to explore the rationales underlying male occurrence in unisexual lineage and evolution of unisexual reproduction. Here, we identified a massively expanded satellite DNA cluster on microchromosomes of hexaploid gibel carp via comparing with the ancestral tetraploid crucian carp (Carassius auratus). Based on the satellite cluster, we developed a method for single chromosomal fluorescence microdissection and isolated three male-specific microchromosomes in a male metaphase cell. Genomic anatomy revealed that these male-specific microchromosomes contained homologous sequences of autosomes and abundant repetitive elements. Significantly, several potential male-specific genes with transcriptional activity were identified, among which four and five genes displayed male-specific and male-biased expression in gonads, respectively, during the developmental period of sex determination. Therefore, the male-specific microchromosomes resembling common features of sex chromosomes may be the main driving force for male occurrence in gynogenetic gibel carp, which sheds new light on the evolution of unisexual reproduction.

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“…Pathway enrichment analysis identified significantly enriched metabolic pathways or signal transduction pathways associated with DTRGs or DTLGs in comparison with the whole genome background. The calculating formula is the same as that used in gene ontology (GO) analysis [74]. The calculated p-value was subjected to FDR correction, using FDR ≤ 0.05 as a threshold.…”

Section: Pathway Enrichment Analysismentioning

confidence: 99%

Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle

Zhang

Zhao

et al. 2021

IJMS

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The turtle carapace is composed of severely deformed fused dorsal vertebrae, ribs, and bone plates. In particular, the lateral growth in the superficial layer of turtle ribs in the dorsal trunk causes an encapsulation of the scapula and pelvis. The recent study suggested that the carapacial ridge (CR) is a new model of epithelial–mesenchymal transition which is essential for the arrangement of the ribs. Therefore, it is necessary to explore the regulatory mechanism of carapacial ridge development to analyze the formation of the turtle shell. However, the current understanding of the regulatory network underlying turtle carapacial ridge development is poor due to the lack of both systematic gene screening at different carapacial ridge development stages and gene function verification studies. In this study, we obtained genome-wide gene transcription and gene translation profiles using RNA sequencing and ribosome nascent-chain complex mRNA sequencing from carapacial ridge tissues of Chinese soft-shell turtle at different development stages. A correlation analysis of the transcriptome and translatome revealed that there were 129, 670, and 135 codifferentially expressed genes, including homodirection and opposite-direction differentially expressed genes, among three comparison groups, respectively. The pathway enrichment analysis of codifferentially expressed genes from the Kyoto Encyclopedia of Genes and Genomes showed dynamic changes in signaling pathways involved in carapacial ridge development. Especially, the results revealed that the Wnt signaling pathway and MAPK signaling pathway may play important roles in turtle carapacial ridge development. In addition, Wnt and Fgf were expressed during the carapacial ridge development. Furthermore, we discovered that Wnt5a regulated carapacial ridge development through the Wnt5a/JNK pathway. Therefore, our studies uncover that the morphogenesis of the turtle carapace might function through the co-operation between conserved WNT and FGF signaling pathways. Consequently, our findings revealed the dynamic signaling pathways acting on the carapacial ridge development of Chinese soft-shell turtle and provided new insights into uncover the molecular mechanism underlying turtle shell morphogenesis.

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Upregulation of the PPAR signaling pathway and accumulation of lipids are related to the morphological and structural transformation of the dragon-eye goldfish eye

Cited by 33 publications

References 84 publications

Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish

Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish

Genomic anatomy of male-specific microchromosomes in a gynogenetic fish

Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle

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