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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS]

ABSTRACT: Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS]

PROVIDER: PRJNA599592 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10850092_1.fastq.gz	Fastqsanger.gz
	SRR10850092_2.fastq.gz	Fastqsanger.gz
	SRR10850093_1.fastq.gz	Fastqsanger.gz
	SRR10850093_2.fastq.gz	Fastqsanger.gz
	SRR10850094_1.fastq.gz	Fastqsanger.gz

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L.

Project description:Integrative analysis of reference epigenomes in polyploid crop Brassica napus L.

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS]

Project description:We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants.

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-seq]

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Project description:Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

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Project description:Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-reChIP]

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-seq]

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L.

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-01-31 | GSE143287 | GEO

Genome dissection in the polyploid crop oilseed rape by transcriptome sequencing

Project description:Many crop species have polyploid genomes that are unlikely to be sequenced to a high standard in the near future, representing a barrier to genomics-based breeding. As an exemplar, we sequenced the leaf transcriptome to analyse both sequence variation1 and transcript abundance across a mapping population of oilseed rape (Brassica napus), together with representatives of ancestors of the parents of the population. Twin SNP linkage maps were constructed, comprising 23,037 markers in all. These were used to analyse the genome for alignment to that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of the progenitor species of B. napus. Methods were developed that enabled us to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an inter-specific cross. This transformative advance, enabling economical high-resolution dissection of the genomes of most, if not all, crop species, will enable us to understand the genetic consequences of breeding and domestication, and will underpin the development of efficient predictive breeding strategies.

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