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Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus

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

ORGANISM(S): Brassica napus Brassica rapa Brassica oleracea

PROVIDER: GSE296743 | GEO | 2025/09/22

REPOSITORIES: GEO

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Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [WGBS]

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 | GSE295119 | GEO

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ATAC-seq]

2025-09-22 | GSE295118 | GEO

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [RNA-seq]

2025-09-22 | GSE295117 | GEO

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ChIP-seq]

2025-09-22 | GSE295116 | GEO

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus

Project description:Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus

| PRJNA1260985 | ENA

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [WGBS]

Project description:Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [WGBS]

| PRJNA1253579 | ENA

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ChIP-seq]

Project description:Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ChIP-seq]

| PRJNA1253576 | ENA

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ATAC-seq]

Project description:Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ATAC-seq]

| PRJNA1253577 | ENA

Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [RNA-seq]

Project description:Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [RNA-seq]

| PRJNA1253575 | ENA

Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in <i>Brassica napus</i> Synthetic Hybrids and Natural Allotetraploid.

Project description:The young allotetraploid Brassica napus (2n = 38, AACC) is one of models to study genomic responses to allopolyploidization. The extraction of AA component from natural B. napus and then restitution of progenitor B. rapa should provide a unique opportunity to reveal the genome interplay for gene expressions during the evolution. Herein, B. napus hybrids (2n = 19, AC) between the extracted and extant B. rapa (2n = 20, AA) and the same B. oleracea genotype (2n = 18, CC) were studied by RNA-seq and compared with natural B. napus donor, to reveal the gene expression changes from hybridization and domestication and the effects of A genome with different origins. Upon the initial merger of two diploid genomes, additive gene expression was prevalent in these two hybrids, for non-additively expressed genes only represented a small portion of total expressed genes. A high proportion of genes exhibited expression level dominance, with no preference to either of the parental genomes. Comparison of homoeolog expressions also showed no bias toward any genomes and the parental expression patterns were often maintained in the hybrids and natural allotetraploids. Although, the overall patterns of gene expression were highly conserved between two hybrids, the extracted B. rapa responded less and appeared more compatible for hybridization than the extant B. rapa. Our results suggested that expression level dominance and homoeolog expressions bias were balanced at the initial stage of genome merger, and such balance were largely maintained during the domestication of B. napus, despite the increased extent over time.

| S-EPMC5061818 | biostudies-literature

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