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Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Tachysurus vachellii Tachysurus fulvidraco Tachysurus fulvidraco x Tachysurus vachelli

PROVIDER: GSE118627 | GEO | 2019/06/12

REPOSITORIES: GEO

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Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [RNA-Seq]

Project description:In this study, we used next-generation sequencing technologies and tandem mass tags to characterize mRNA-seq, miRNA-seq and proteomic of Pelteobagrus fulvidraco, P. vachelli and hybrid yellow catfish Huangyou-1 (P. fulvidraco female×P. vachelli male) livers and in doing so, offer deeper insight into the transcriptional and protein changes in heterosis uncovers key roles for miRNAs.

2019-06-12 | GSE118626 | GEO

Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [miRNA-Seq]

Project description:In this study, we used next-generation sequencing technologies and tandem mass tags to characterize mRNA-seq, miRNA-seq and proteomic of Pelteobagrus fulvidraco, P. vachelli and hybrid yellow catfish Huangyou-1 (P. fulvidraco female ×P. vachelli male) livers and in doing so, offer deeper insight into the transcriptional and protein changes in heterosis uncovers key roles for miRNAs.

2019-06-12 | GSE118625 | GEO

Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis.

Project description:Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.

| S-EPMC6601203 | biostudies-literature

Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs

Project description:Heterosis is a complex biological phenomenon in which hybridization exhibit superior phenotypic characteristics. The underlying molecular basis for heterosis, particularly for fishes, remains elusive. In this study, we used next-generation sequencing technologies and tandem mass tags to characterise mRNA-seq, miRNA-seq and proteomic of Pelteobagrus fulvidraco, P. vachelli and hybrid yellow catfish Huangyou-1 (P. fulvidraco ♀×P. vachelli ♂) livers and in doing so, offer deeper insight into the transcriptional and protein changes in heterosis uncovers key roles for miRNAs.

2019-05-15 | PXD010728 |

Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs

Project description:Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs

| PRJNA486270 | ENA

Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [RNA-Seq]

Project description:Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [RNA-Seq]

| PRJNA486274 | ENA

Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [miRNA-Seq]

Project description:Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [miRNA-Seq]

| PRJNA486275 | ENA

Sex-biased miRNAs in gonad and their potential roles for testis development in yellow catfish.

Project description:Recently, YY super-male yellow catfish had been created by hormonal-induced sex reversal and sex-linked markers, which provides a promising research model for fish sex differentiation and gonad development, especially for testis development. MicroRNAs (miRNAs) have been revealed to play crucial roles in the gene regulation and gonad development in vertebrates. In this study, three small RNA libraries constructed from gonad tissues of XX female, XY male and YY super-male yellow catfish were sequenced. The sequencing data generated a total of 384 conserved miRNAs and 113 potential novel miRNAs, among which 23, 30 and 14 miRNAs were specifically detected in XX ovary, XY testis, and YY testis, respectively. We observed relative lower expression of several miR-200 family members, including miR-141 and miR-429 in YY testis compared with XY testis. Histological analysis indicated a higher degree of testis maturity in YY super-males compared with XY males, as shown by larger spermatogenic cyst, more spermatids and fewer spermatocytes in the spermatogenic cyst. Moreover, five miR-200 family members were significantly up-regulated in testis when treated by 17α-ethinylestradiol (EE2), high dose of which will impair testis development and cell proliferation. The down-regulation of miR-141 and 429 coincides with the progression of testis development in both yellow catfish and human. At last, the expression pattern of nine arbitrarily selected miRNAs detected by quantitative RT-PCR was consistent with the Solexa sequencing results. Our study provides a comprehensive miRNA transcriptome analysis for gonad of yellow catfish with different sex genotypes, and identifies a number of sex-biased miRNAs, some of that are potentially involved in testis development and spermatogenesis.

| S-EPMC4168133 | biostudies-literature

The Analysis of RNA-Sequencing Reveals the Immune Regulatory Roles of Key MiRNAs in Intestines of the Hybrid Yellow Catfish (Tachysurus fulvidraco♀ * P. vachellii♂) under transport stress

Project description:The miRNA negatively regulation of target genes expression indicated the immune role of integrating miRNA with mRNA targets may through TNF alpha-mediated pathways regulated immune response and intestinal injury under transport stress.

2022-11-13 | GSE217522 | GEO

The parallel reaction monitoring assays in heterosis of hybrid yellow catfish Huangyou-1

Project description:Heterosis is a complex biological phenomenon in which hybridization exhibits superior phenotypic characteristics. The underlying molecular basis for heterosis, particularly for fishes, remains elusive. The utilization rate of fish heterosis far exceeds our understanding of it on a theoretical level. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we characterized mRNA-seq, miRNA-seq, and proteomes of Pelteobagrus fulvidraco, P. vachelli, and the hybrid yellow catfish Huangyou-1 (P. fulvidraco ♀×P. vachelli ♂) livers using next-generation sequencing technologies and tandem mass tags. Our results show that the nonadditive, homoeologue expression bias and expression level dominance pattern were readily identified in transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. At the same time, a number of miRNA-mRNA-protein pairs were found and validated by qRT-PCR and parallel reaction monitoring assays.

2019-04-26 | PXD011343 |

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