Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat
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ABSTRACT:
PROVIDER: PRJNA793259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17386100_1.fastq.gz | Fastqsanger.gz | |||
| SRR17386100_2.fastq.gz | Fastqsanger.gz | |||
| SRR17386200_1.fastq.gz | Fastqsanger.gz | |||
| SRR17386200_2.fastq.gz | Fastqsanger.gz | |||
| SRR17386101_1.fastq.gz | Fastqsanger.gz |
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Project description:Common wheat (T. aestivum) converged three subgenomes adapted to different environments. The combinatorial interaction between transcription factors (TFs) and regulatory elements (REs) defines a regulatory circuit that underlies subgenome convergence and divergence. Compared to the relatively conserved gene composition across subgenomes, the intergenic regions with abundant REs is drastically diversified by almost complete TE turnovers, raising major questions regarding how subgenome convergent and divergent regulation is encoded in the highly diversified intergenic regions, and the impact of TE evolution on regulatory conservation and innovation. In the present study, we created genome-wide TF binding catalog to assemble an extensive wheat regulatory network comprising connections among 182 TFs. The different effects of ancient and recent TE insertions on regulatory specificity were observed. Subgenome asymmetric TE expansion is an important source of subgenome divergent TFBS, which help explain the vast occupancy difference across subgenomes. Interestingly, the ancient expansion of RLC_famc1.4-derived TFBS occurred in more than 25% triads promoters. A significant fraction of these TE-derived TFBS subjected to region-specific evolutionary selections, resulting in subgenome-balanced TF binding but unbalanced degeneration of flanking TE sequences. These TE-derived subgenome convergent and divergent regulation linked to subgenome conserved and diversified pathways, suggesting that TEs are an important regulatory driving force contributed to polyploid evolution. Overall, this study demonstrated the impact of TEs on shaping the plasticity and adaptation of common wheat, enriched the theories of TE-promoted transcriptional innovation from the evolutionary aspects of polyploid regulation since first reported by McClintock.
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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: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: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: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:The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid.
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Project description:Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development
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Project description:Transcription start site (TSS) is the hub integrating regulatory input from promoters and enhancers. Common wheat converged three subgenomes adapted to different environment and established as a major crop worldwide. Detection of more precise and new TSS of both genes and enhancers in common wheat is the basis in interpreting transcriptional regulatory networks as well as the subgenome divergent regulation in their entirety.
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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.
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