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ABSTRACT: RNA-seq for SlGRAS4 chilling treatment in tomato fruit

PROVIDER: PRJNA594085 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10601162.fastq.gz	Fastqsanger.gz
	SRR10601163.fastq.gz	Fastqsanger.gz
	SRR10601164.fastq.gz	Fastqsanger.gz
	SRR10601165.fastq.gz	Fastqsanger.gz
	SRR10601166.fastq.gz	Fastqsanger.gz

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Project description:Tomato fruit chilling stress

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Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis

Project description:To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4M-BM-0C/4M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25M-BM-0C/20M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h)leaves of LA1777M-bM-^@M-^Y (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. 161 conserved miRNAs and 236 novel miRNAs were identified in the two librayies. Of these miRNAs, 192 were upregulated, whereas 205 were downregulated in response to chilling stress. Among these, 23 miRNAs and 26 miRNAs were significantly upregulated and downregulated in response to chilling stress, respectively.Through degradome sequencing,62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Target gene functional analysis revealed that most target genes played positive role in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzymes and genes involved in cell wall formation. tomato miRNA-seq and Degradome-seq after chilling

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Project description:Tomato fruit are susceptible to postharvest chilling injury when stored at low temperature, thus result in quality deterioration and economic losses worldwide. Protein phosphorylation is an important post-translational modification, which is proven to be involved in plant cold tolerance. But the protein phosphorylation underlying cold stress responses in tomato fruit are remains poorly understood. In this study, we perform comparative phosphoproteomics and provide an overall phosphoprotein profiles in tomato fruit after postharvest cold storage and subsequent shelf-life. A total of 10260 phosphopeptides corresponding to 9640 phosphosites in 3740 phosphoproteins were identified.

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Project description:RNA-seq of tomato fruit

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Project description:RNA-Seq of tomato fruit

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Project description:Most crops are from tropical origin and, consequently, chilling sensitive. However, some tropical plants, are able to augment their chilling tolerance in response to suboptimal growth temperatures. Yet, the molecular and physiological mechanisms underlying this response still remain unclear. Here, we demonstrate that tomato plants can develop a chilling acclimation response and document the comprehensive transcriptomic and metabolic adjustments leading to the increase in chilling tolerance.

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Project description:RNA-Seq of peach fruit sujected to chilling injury

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Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [ChIP-Seq]

Project description:Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. A large number of the SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation, pigment biosynthesis, and hormone signaling. Fourteen ripening-related genes including RIN, ACS4, ACO1, PL, TBG4 were confirmed to be directly regulated by SlJMJ6 through removing H3K27me3. Taken together, these results indicated that SlJMJ6 is a ripening prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating fruit ripening in tomato. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.

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