Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1087715 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28342900_1.fastq.gz | Fastqsanger.gz | |||
| SRR28342900_2.fastq.gz | Fastqsanger.gz | |||
| SRR28342901_1.fastq.gz | Fastqsanger.gz | |||
| SRR28342901_2.fastq.gz | Fastqsanger.gz | |||
| SRR28342902_1.fastq.gz | Fastqsanger.gz |
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Project description:The importance and applications of polyploidy have long been recognized, from shaping the evolutionary success of flowering plants to improving agricultural productivity. Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. How quickly one subgenome dominates within a newly formed polyploid, if immediate or after millions of years, and the genomic features that determine which genome dominates remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and that subgenome expression dominance significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within transposons in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and submissive subgenomes in the natural allopolyploid. Our analyses reveal that the subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following the hybridization. These findings not only provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events, but may also contribute to uncovering the mechanistic basis of heterosis and subgenomic dominance.
2018-05-23 | GSE95799 | GEO
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295117 | GEO
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295118 | GEO
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
2025-09-22 | GSE295116 | GEO
Project description:Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.
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Project description:Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower
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Project description:Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. rapa and B. oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-seq analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12,709 DAS events) and lower in resynthesized Brassica napus (8,863 DAS events). Natural B. napus had more up-regulated events and fewer down-regulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in natural and resynthesized B. napus, and indicate that abiotic stress can influence the evolution of homeologous genes in polyploids.
2023-02-04 | GSE201225 | GEO