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

PROVIDER: PRJNA486270 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7702270.fastq.gz	Fastqsanger.gz
	SRR7702280_1.fastq.gz	Fastqsanger.gz
	SRR7702280_2.fastq.gz	Fastqsanger.gz
	SRR7702271.fastq.gz	Fastqsanger.gz
	SRR7702281_1.fastq.gz	Fastqsanger.gz

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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

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 [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]

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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]

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Environmental dependent heterosis and transgressive gene expression in reciprocal hybrids between the channel catfish Ictalurus punctatus and the blue catfish Ictalurus furcatus

Project description:The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.

2022-01-05 | GSE186603 | GEO

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-12 | GSE118627 | 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 |

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.

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Yellow catfish brain exposure to hypoxia

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