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Solanum lycopersicum

ABSTRACT: Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing

PROVIDER: PRJNA213528 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR943813.fastq.gz	Fastqsanger.gz
	SRR943814.fastq.gz	Fastqsanger.gz
	SRR943815.fastq.gz	Fastqsanger.gz
	SRR943816.fastq.gz	Fastqsanger.gz
	SRR943817.fastq.gz	Fastqsanger.gz

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Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing

Project description:The tomato MADS-box FRUITFULL (FUL) homologs, FUL1 and FUL2, interact with the main ripening regulator RIPENING INHIBITOR (RIN). To clarify their role in fruit ripening, we generated FUL1/FUL2-suppressed transgenic lines by RNAi. We found that five transgenic lines bearing fruits that did not ripen normally: lycopene accumulation and increase of ethylene production were severely inhibited. We then performed next generation RNA sequencing (RNA-Seq) analysis of the fruits of a FUL1/FUL2-suppressed line (TF18) with those of the wild type (Ailsa Craig cultivar; AC) and rin mutant. The comparison of RNA-Seq data among them indicated that FUL1/FUL2-suppression significantly affected the expression of a larger portion of ripening-induced and -repressed genes than the rin mutation did. Moreover, the effect of FUL1/FUL2-suppression was observed not only in the fruits harvested at the wild type ripening age [45 days after pollination (DAP)] but also in those at the pre-ripening age (35 DAP). This suggests that the FUL homologs play an essential role in the regulation of fruit development and ripening, the role which covers a wider range of biological processes than RIN does. Differentially expressed genes (DEGs) between the wild type and TF18 fruits included known ripening-related genes such as ACS2 and ACS4 involved in ethylene production and PSY1 in carotenoid biosynthesis, consistent with the phenotype of TF18 fruits described above. The DEGs also included many direct RIN target genes, which supports the hypothesis that the FUL homologs regulate fruit ripening in a form of MADS-box complex with RIN. mRNA profiles of wild type (Ailsa Craig cultivar), rin mutant and FUL1/FUL2-suppressed tomato fruits harvested at 35DAP and 45 DAP were generated by next generation sequencing, in triplicate, using Illumina Hiseq2000.

2014-06-23 | E-GEOD-49289 | biostudies-arrayexpress

Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing

2014-06-23 | GSE49289 | GEO

Solanum lycopersicum strain:Ailsa Craig-derived mutants

Project description:Transcriptome profiling of tomato fruits of allelic mutants in the RIN locus by next generation RNA sequencing

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High-throughput pyrosequencing of endogenous small RNAs from Solanum lycopersicum leaf and fruit

Project description:Comparison of the endogenous small RNA content of tomato leaves and fruits.

2008-08-22 | GSE12081 | GEO

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Project description:Microarray analysis of ripening tomato fruits with RNAi knockdown of a direct RIN-target GRAS family gene

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Project description:Transcriptome profiling of very-early-harvested tomato fruits

| PRJNA1102113 | ENA

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Project description:Comparative gene expression analysis in fruits of a tomato introgression line performing higher ascorbic acid content

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Project description:Global transcriptomic changes induced by manipulate MSH1 gene in tomato using next generation sequencing

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Project description:Next Generation Sequencing of tomato WT, M82 and pro∆GRAS mutant treated with Gibberellin

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Microarray analysis of ripening tomato fruits with RNAi knockdown of a direct RIN-target GRAS family gene

Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening. We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown. RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally. However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism. This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato.

2014-03-01 | GSE45658 | GEO

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