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Solanum pimpinellifolium

ABSTRACT: Identification of miRNAs and their targets in tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis

PROVIDER: PRJNA292128 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2148663.fastq.gz	Fastqsanger.gz
	SRR2148664.fastq.gz	Fastqsanger.gz
	SRR2148665.fastq.gz	Fastqsanger.gz
	SRR2148666.fastq.gz	Fastqsanger.gz
	SRR2148667.fastq.gz	Fastqsanger.gz

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Identification of miRNAs and their targets in tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis

Project description:MicroRNAs (miRNAs) are 19-24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18°C, 33/33°C and 40/40°C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of four miRNAs and five target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures.

2016-12-01 | GSE71819 | GEO

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Project description:Tomato raw sequence reads

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Expression of genes in red fruit of Andean tomato (Solanum lycopersicum) and Solanum pimpinellifolium

Project description:In this study, we explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor S. pimpinellifolium. The goal is to shed light in understanding the factors responsible for acquiring tomato fruit quality (taste and flavour) at molecular level during the domestication process.

2019-09-10 | GSE125476 | GEO

Identification of MicroRNAs and Their Targets in Tomato Infected with Cucumber Mosaic Virus

Project description:We constructed two independent small RNA libraries from leaves of mock and Cucumber mosaic virus (CMV) infected tomatoes, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 known miRNAs (32 families) and 568 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 known miRNAs and 154 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed 79 miRNAs (including 15 novel tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries. Among these virus responsive miRNAs, expression patters of some novel tomato miRNAs and PC-miRNAs in mock and in CMV-Fny infected tomatoes were further validated by qRT-PCR. Moreover, we revealed 563 potential targets for 66 tomato miRNAs by the recently developed degradome sequencing approach, including 124 targets for 7 new tomato miRNAs and 97 targets for 24 PC-miRNAs. Target annotation for the newly identified miRNA and PC-miRNAs indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that stress response- and photosynthesis-related genes were most affected in CMV-Fny infected tomatoes. Examination of small RNAs and their targets in mock and CMV-Fny infected tomatoes.

2014-10-20 | E-GEOD-56974 | biostudies-arrayexpress

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Project description:Abscisic acid regulates plant growth and flowering through SINGLE FLOWER TRUSS pathway in tomato.

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Identification of MicroRNAs and Their Targets in Tomato Infected with Cucumber Mosaic Virus

2014-10-20 | GSE56974 | GEO

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Project description:The Zinc Finger Transcription Factor SlZFP2 Negatively Regulates Abscisic Acid Biosynthesis and Fruit Ripening in Tomato

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Solanum pimpinellifolium

Project description:Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape

| PRJNA115951 | ENA

Solanum lycopersicum, Solanum pimpinellifolium

Project description:Bulk segregant analysis for lateral root length and number in tomato

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Dissection of the style’s response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species

Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species.

2015-04-09 | GSE67654 | GEO

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