Ontology highlight
ABSTRACT:
PROVIDER: PRJNA603155 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10967500_1.fastq.gz | Fastqsanger.gz | |||
| SRR10967500_2.fastq.gz | Fastqsanger.gz | |||
| SRR10967501_1.fastq.gz | Fastqsanger.gz | |||
| SRR10967501_2.fastq.gz | Fastqsanger.gz | |||
| SRR10967502_1.fastq.gz | Fastqsanger.gz |
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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: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: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.
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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.
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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
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Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
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Project description:Melon (Cucumis melo L.) is the model species of the Cucurbitaceae family and an important crop, with an estimated production at 28 million tonnes in 2020. However, its yield is primarily affected by viruses. Cucumber mosaic virus (CMV) is particularly significant due to its broad host range, capable of infecting over 100 plant families. Resistance to CMV in the melon accession Songwhan Charmi (SC) is controlled by the recessive gene cmv1, which encodes the Vacuolar Protein Sorting 41, involved in vesicle transport to the vacuole. cmv1 restricts the virus to the bundle sheath cells and impedes viral access to the phloem, and this phenotype depends on the viral movement protein (MP). However, little is known about the broader cellular changes that CMV triggers in melon or the specific biological responses that facilitate or restrict the virus' entry into the phloem in susceptible and resistant varieties. We profiled the proteomes of CMV-resistant or susceptible melon genotypes inoculated with LS or FNY strains. Analysis of co-abundance networks revealed pathways involved in CMV resistance and susceptibility at different infection stages. Upon inoculation, resistant varieties have stronger changes in proteome composition compared to susceptible varieties, including an increase in lipid signalling and upregulation of phloem defence proteins. In contrast, susceptible melon plants displayed fewer proteins related to translation, photosynthesis and intracellular transport. During the systemic infection of susceptible melon plants, proteins associated with stress responses increase, such as those involved in the ER-associated degradation (ERAD) and phenylpropanoid pathways. Collectively, our study shed new light on the interactions between CMV and melon plants.
2025-04-08 | PXD059006 | Pride
Project description:Purpose: We conducted a reverse genetic approach in order to elucidate the role of H3K27me3 writers and erasers in the process of sex determination and expression in melon. Methods: We used TILLING to find loss-of function mutants of cmLHP1 proteins in melon. Selected alleles were phenotyped at the developmental and molecular levels. We generated the cmlhp1ab mutant, for which we observed a pleiotropic phenotype. For this double mutant, we integrated RNA-seq (leaves), ChIP-seq (leaves) and RT-PCR (flowers) for elucidating the impact of cmLHP1 loss of function at the molecular level. Results: cmlhp1ab displayed a pleiotropic phenotype which correlated with genome-wide changes of H3K27me3 (moore oftenly hypomethylation) and deregulation of genes involved in flower development and hormone responses.
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