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Global increase in DNA Methylation during ripening of sweet orange [RNA-seq]

ABSTRACT: Global increase in DNA Methylation during ripening of sweet orange [RNA-seq]

PROVIDER: PRJNA429187 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6451540_1.fastq.gz	Fastqsanger.gz
	SRR6451540_2.fastq.gz	Fastqsanger.gz
	SRR6451531_1.fastq.gz	Fastqsanger.gz
	SRR6451531_2.fastq.gz	Fastqsanger.gz
	SRR6451541_1.fastq.gz	Fastqsanger.gz

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Global increase in DNA Methylation during ripening of sweet orange [ncRNA-seq]

Project description:Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.

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Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in five fruit ripening stages in sweet orange

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Global increase in DNA Methylation during ripening of sweet orange

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Project description:Global increase in DNA Methylation during ripening of sweet orange [BS-seq]

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Transcriptome dynamics during fruit development of sweet orange (Citrus sinensis)

Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits. Investigate the transcriptome changes during five fruit developmental stages of two sweet orange genotypes

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Genome-wide profiling of microRNAs in sweet orange

Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs. Small RNA sequencing of the leaves and flowers in sweet orange

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Global increase in DNA Methylation during ripening of sweet orange

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

2018-12-28 | GSE120026 | GEO