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Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids

ABSTRACT: Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids

OTHER RELATED OMICS DATASETS IN: GSE50715

PROVIDER: PRJNA218556 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR974894.fastq.gz	Fastqsanger.gz
	SRR974895.fastq.gz	Fastqsanger.gz
	SRR974896.fastq.gz	Fastqsanger.gz
	SRR974897.fastq.gz	Fastqsanger.gz
	SRR974898.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids

Project description:Polyploidy provides evolutionary and morphological novelties in many plants and some animals. However, the role of genome dosage and composition in gene expression changes remains poorly understood. Here, we generated a series of resynthesized Arabidopsis tetraploids that contain 0-4 copies of Arabidopsis thaliana and Arabidopsis arenosa genomes and investigated ploidy and hybridity effects on gene expression. Allelic expression can be defined as dosage dependent (expression levels correlate with genome dosages) or otherwise as dosage independent. Here, we show that many dosage-dependent genes contribute to cell cycle, photosynthesis, and metabolism, whereas dosage-independent genes are enriched in biotic and abiotic stress responses. Interestingly, dosage-dependent genes tend to be preserved in ancient biochemical pathways present in both plant and nonplant species, whereas many dosage-independent genes belong to plant-specific pathways. This is confirmed by an independent analysis using Arabidopsis phylostratigraphic map. For A. thaliana loci, the dosage-dependent alleles are devoid of TEs and tend to correlate with H3K9ac, H3K4me3, and CG methylation, whereas the majority of dosage-independent alleles are enriched with TEs and correspond to H3K27me1, H3K27me3, and CHG (H = A, T, or C) methylation. Furthermore, there is a parent-of-origin effect on nonadditively expressed genes in the reciprocal allotetraploids especially when A. arenosa is used as the pollen donor, leading to metabolic and morphological changes. Thus, ploidy, epigenetic modifications, and cytoplasmic-nuclear interactions shape gene expression diversity in polyploids. Dosage-dependent expression can maintain growth and developmental stability, whereas dosage-independent expression can facilitate functional divergence between homeologs (subfunctionalization and/or neofunctionalization) during polyploid evolution.

2015-05-19 | GSE50715 | GEO

Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids.

| S-EPMC6281156 | biostudies-literature

Genome-wide gene/genome dosage imbalance regulates gene expressions in synthetic Brassica napus and derivatives (AC, AAC, CCA, CCAA)

Project description:Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remains poorly understood. Herein, the serial Brassica hybrids/polyploids with different dosages of A and C subgenomes were synthesized to investigate the effects of genome dosages on gene expressions and interaction using RNA-Seq. The expression changes of A- and C-subgenome genes were in accordance with dosage alterations. Dosage-dependent and -independent genes were grouped according to the correlations between dosage variations and gene expressions. Expression levels of dosage-dependent genes were strongly correlated with dosage changes that mainly contributed to dosage effects, while those of dosage-independent genes gave weak correlations with dosage variations that mostly facilitated dosage compensation. More protein–protein interactions were detected for dosage-independent genes than dosage-dependent ones, as predicted by the dosage balance hypothesis. Dosage-dependent genes more likely impacted the expressions by trans effects, whereas dosage-independent genes preferred to play by cis effects. Furthermore, dosage-dependent genes were mainly associated with the basic biological processes to maintain the stability of the growth and development, while dosage-independent genes were more enriched in the stress response related processes to accelerate adaptation. The present comprehensive analysis of gene expression dependent/independent on dosage alterations in Brassica polyploids provided new insights into gene/genome dosage-imbalance regulation of gene expression.

2016-05-25 | GSE81845 | GEO

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

Project description:Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

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Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

Project description:Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

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Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

Project description:Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

| PRJEB23787 | ENA

Origin of extra-embryonic mesenchyme points to evolutionary novelty in primate early development

Project description:Origin of extra-embryonic mesenchyme points to evolutionary novelty in primate early development

| PRJNA911737 | ENA

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [aCGH]

Project description:Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [aCGH]

| PRJNA420103 | ENA

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [expression]

Project description:Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [expression]

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DEEP CONVERGENCE, SHARED ANCESTRY AND EVOLUTIONARY NOVELTY IN THE GENETIC ARCHITECTURE OF HELICONIUS MIMICRY

Project description:DEEP CONVERGENCE, SHARED ANCESTRY AND EVOLUTIONARY NOVELTY IN THE GENETIC ARCHITECTURE OF HELICONIUS MIMICRY

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