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LHP1-mediated conditional repression of subgenome-diversified defenses is responsible for the high plasticity of allopolyploid wheat

ABSTRACT: LHP1-mediated conditional repression of subgenome-diversified defenses is responsible for the high plasticity of allopolyploid wheat

PROVIDER: PRJNA904271 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22378000_1.fastq.gz	Fastqsanger.gz
	SRR22378000_2.fastq.gz	Fastqsanger.gz
	SRR22377978_1.fastq.gz	Fastqsanger.gz
	SRR22377978_2.fastq.gz	Fastqsanger.gz
	SRR22377979_1.fastq.gz	Fastqsanger.gz

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LHP1-mediated conditional repression of subgenome-diversified defenses is responsible for the high plasticity of allopolyploid wheat

Project description:High plasticity of common wheat is attributed to the captured and polyploidization-promoted diversity. However, uncontrolled subgenome diversification can lead to hybrid conflict and dysgenesis, resulting in decreased diversity. How genomic diversity is maintained and interpreted to increase plasticity is unclear. By data-mining from the binding of 193 genome-wide trans-factors and genetic perturbations in common wheat, we identified LHP1 as a major regulator of subgenome-diversified defense genes, enhancer RNAs, and metabolite synthesis-related gene clusters via H3K27me3. Stripe rust infection leads to a global decrease in LHP1-mediated H3K27me3, deprivation of which enhances common wheat stripe rust resistance. We also revealed the consistency between subgenome diversity and population diversity, potentially promoted by LHP1, implying the recent diversification preferentially occurred in the captured subgenome-diversified regions regulated by LHP1. Thus, common wheat benefitted from multi-faced role of LHP1 in promoting sequence diversity and repressing subgenome-diversified defenses; this constraint is eliminated by pathogen infections, enabling timely release and fixation of favorable variations, conferring the evolutionary advantage and high plasticity of common wheat.

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Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower

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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Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat

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The Arabidopsis GAGA-binding factor BPC6 recruits PRC1 component LHP1 to GAGA DNA-motifs

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