Ontology highlight
ABSTRACT:
PROVIDER: PRJNA875218 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21363518_1.fastq.gz | Fastqsanger.gz | |||
| SRR21363518_2.fastq.gz | Fastqsanger.gz | |||
| SRR21363519_1.fastq.gz | Fastqsanger.gz | |||
| SRR21363519_2.fastq.gz | Fastqsanger.gz | |||
| SRR21363520_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: MicroRNAs (miRNAs) represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Although Hami melon is an attractive model for valuable biological traits analysis, the role of miRNA action in the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the Hami melon miRNA profiles at four fruit developmental stages Results: Small RNA sequencing yielded raw reads in eight libraries. miRNAs expression profiles were variable at different fruit developmental stages. The expression levels of five known miRNAs were validated by quantitative real-time PCR. Among the identified miRNAs, several miRNAs showed developmentally regulated and differentially expressed pattern during fruit development. Conclusions: Our results present a first comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis for further research on the critical role of miRNAs in melon fruit development.
2017-09-06 | GSE77127 | GEO
Project description:Purpose: the goals of this study are to compare fruit of two clitivars oriental melon transcriptome profiling (RNA-seq) at different stages to explore carotenoid potentail carotenoid accumulation mechanism Methods:The transcriptome sequence of two cultivars oriental melon fruits at different stages were generated by deep sequencing with three repeats using Illumina. The sequence reads that passed filters were mapped to melon genome (http://cucurbitgenomics.org/organism/18) using HISAT2 software. The differently expressed genes were identify by |log2(FoldChange)| > 0 & padj <= 0.05, and qRT–PCR validation was performed using SYBR Green assays Result:Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the melon genome. The differentially expressed genes were functionally classified by GO and KEGG enrichment. We focused on carotenoid metabolism related gene and validated using qRT-PCR. The results showed RNA-seq and qRT-PCR were highly correlated. Conclusion: Our study provided transcriptome sequence of oriental melon fruits at different stages in two cultivars. The optimized data analysis workflows reported here should provide comparative framework of expression profiles. Our transcriptome characterization contribute to analyze gene functions and metabolic process of oriental melon.
2022-01-13 | GSE193412 | GEO
Project description:RNA-Seq was conducted among sergeant bulks of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg), a total of about 105 million reads were generated from the melon transcriptome using Solexa sequencing.Totally 79,698 unigenes were generated and 75,537 unigenes were mapped to 11,805 annotated proteins in assembled melon genome (Garcia-Mas et al., 2012). Transcripts related to photomorphogenesis and flower development in plants were found, Most of the genes encoding plant hormone metabolism related protein, others related to flora development including Tasselseeds and male sterility genes which in phytohormones pathway were also detected. Comparison each two bulks (AAGG:AAgg, AAGG:aaGG, aagg:AAgg and aaGG:aagg ) exhibited different profiles of putative genes (include 745, 1342, 858 and 571 different expression genes, respectively). mRNA profiles of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg) were were generated by deep sequencing using Illumina Hiseq 2000.
2014-06-15 | E-GEOD-57580 | biostudies-arrayexpress
Project description:Virus resistances that are recessively inherited are associated with loss-of-susceptibility resistance alleles. Resistance to Watermelon mosaic virus (WMV) of melon accession TGR-1551 is expressed as a drastic reduction of the virus titer, and is recessively inherited. In this work, viral RNA accumulation was measured in TGR-1551 and in susceptible WMV-infected melon plants by real time quantitative PCR (qPCR), and gene expression of 17,443 unigenes represented in a melon microarray was monitored in a time-course experiment. Virus accumulation was higher in inoculated cotyledons of the resistant genotype up to 7 days post-inoculation; from this time on, virus accumulation was much higher in plants of the susceptible genotype. Microarray experiments were carried with samples from inoculated cotyledons at 1 and 3 dpi to monitor early changes in response to virus infection, and at 7 dpi. Samples from systemically infected leaves harvested at 15 dpi were also included in the analysis. Results showed much more profound transcriptomic alterations in resistant plants compared to susceptible ones. Analyses of gene expression profiles reveal deep and extensive transcriptomic alterations in TGR-1551 plants, many of them involving pathogen response-related genes. Overall, data suggested that resistance to WMV in TGR-1551 is associated with a defense response, contrasting with its recessive nature. Two melon genotypes have been used to analyse transcriptomic responses to infection by Watermelon mosaic virus: Tendral (susceptibel to WMV) and TGR-1551 (resistant to WMV). For each genotype, 60 melon seedlings were inoculated with WMV-M116 and another 60 were mock-inoculated. Cotyledons of 10 plants were harvested at 1, 3, 5, 7, 9 and 15 dpi. At 15 dpi, the systemically infected second true leaf was also harvested. To reduce variability, each biological replicate used in this study was prepared by mixing the RNA extracts from 2 or 4 mock or WMV-inoculated cotyledons, respectively, or from 3 melon leaves. Samples (WMV infected and mock inoculated) corresponding to cotyledons at 1, 3 and 7 dpi, and leaves at 15 dpi were used for microarray hybridisations, three biological replicates for each one, leading to a total of 48 samples.
2011-10-02 | E-GEOD-30111 | biostudies-arrayexpress
Project description:This study was designed to identify the sRNAs in Aphis gossypii (cotton-melon aphid) during Vat-mediated resistance in teraction with melon
2013-06-01 | GSE38641 | GEO
Project description:Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21â24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analyzed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. This analysis provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melonâvirus interactions.
2011-08-03 | GSE28653 | GEO
Project description:Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21â24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analyzed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. This analysis provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melonâvirus interactions. 11 small RNA libraries from several tissues of melon are included en the raw data. 2 samples from ovary, 2 samples from fruit, 1 sample from healthy cotyledons (Cultivar Tendral), 1 samples from healthy cotyledons (genotype TGR-1551), 1 sample from cotyledons (cultivar Tendral) infected with Watermelon mosaic virus (WMV), 1 sample from cotyledons (cultivar TGR-1551) infected with WMV, 1 sample from cotyledons (cultivar Tendral) infected with Melon necrotic spot virus (MNSV, Malfa5 isolate), 1 sample from cotyledons (cultivar Tendral) infected with MNSV (chimeric virus with Malfa5-264 isolates), 1 library from synthetic RNA oligos. Raw reads were obtained from two independent 454 runs, ~22,000 reads each one, to a total of 447,180 reads
2011-08-03 | E-GEOD-28653 | biostudies-arrayexpress
Project description:Subsequently, using a combination of BSA-seq, transcriptomic sequencing (RNA-seq), and proteomic sequencing approaches, we identified the candidate gene Nitab4.5_0008674g0010 that encodes dihydroneopterin aldolase as a factor associated with tobacco leaf yellowing.
2024-06-15 | PXD053162 |
Project description:This study was designed to identify the sRNAs in Aphis gossypii (cotton-melon aphid) during Vat-mediated resistance in teraction with melon Methods: Whole insects were collected from susceptible (Vat-) and resistant (Vat+) plants after 48 hours of feeding. Total RNA was extracted from the aphids and enriched for LMW RNA and small RNA libraries were constructed using standard protocols and deep sequenced using Illumina GAII analyzer.
2013-06-01 | E-GEOD-38641 | biostudies-arrayexpress