Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR128721.fastq.gz | Fastqsanger.gz | |||
| ERR128722.fastq.gz | Fastqsanger.gz | |||
| ERR128725.fastq.gz | Fastqsanger.gz | |||
| ERR128726.fastq.gz | Fastqsanger.gz | |||
| ERR129968.fastq.gz | Fastqsanger.gz |
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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.
2011-08-03 | GSE28653 | GEO
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of cucumis melo seeds and leaves to the treatment with B. subtilis cells or the secondary metabolite fengycin
2022-04-20 | GSE175611 | 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:Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing
| PRJNA138849 | ENA
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:One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different individuals can reveal differences between them (single-feature polymorphisms (SFPs)). These SFPs can be used as markers for breeding purposes, or they can be converted to conventional markers by sequencing. This method has been utilized in a few different plants to discover genetic variation using Affymetrix arrays that exist for only a few organisms. We applied this approach, with some modifications, for marker discovery in melon. For marker discovery, we used DNA from the parents of our mapping population, developed by Katzir's group from a cross between representatives of two subspecies of Cucumis melo L.: PI414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Two biological replicates from PI414723 and two from 'Dulce' were used. Each biological replicate contained gDNAs pooled from 10 different plants. gDNA samples were labeled and hybridized using standard Agilent procedures for comparative genomic hybridization (CGH). The inter-population genetic variation was detected using two arrays, with one of the biological replicates of 'Dulce' against one of the PI414723 replicates on each array. The intra-population variation was detected by hybridizing the PI414723 replicates against each other and the 'Dulce' replicates against each other. Intra-population variation was estimated to ensure that the genetic variation between these populations is based on alleles that are fixed in the population and not due to intra-population variation.
2010-08-01 | E-GEOD-17673 | biostudies-arrayexpress
Project description:<p>Grafting is widely applied in the cultivation of melon. In this study, 'Qinmi No.1' [<em>Cucumis melo </em>L.<em> </em>(QG)] and 'Ribenxuesong' [<em>Cucurbita maxima</em> Duch. (RG)] were used as rootstocks for 'QingxinYangjiaocui' (<em>Cucumis melo</em> L.). The results showed that grafting with muskmelon rootstocks had no significant effect on fruit aroma, but grafting with pumpkin rootstocks significantly reduced the odor intensity and odor preference scores of melon fruits. Compared with the fruits from self-grafted plants (SG), four new aromatic volatiles with a sweet smell were detected, the alcohol dehydrogenase (ADH) activity was significantly decreased at 30 DAP, but unaffected at 42 DAP in QG fruits. There was no difference for alcohol acetyltransferase (AAT) activity between QG and SG fruits. The expression level of CmADH2 was significantly higher at 30 DAP and 42 DAP, but CmAAT2 was significantly lower at 42 DAP in QG fruits compared with SG fruits. In RG fruits, the main aroma compounds including butanoic acid ethyl ester, 2-methyl-2-butenal and 2-methylheptan-1-al were absent, while the volatile compounds with unpleasant odor characteristics including trans, cis-2,6-nonadien-1-ol, (E,E)-2,4-heptadienal, octanoic acid and styrene were detected. Compared with SG fruits, 1-nonanol and 1-heptanol with green odor characteristics were significantly increased, but eucalyptol and farnesene with fruity aroma characteristics were significantly decreased in RG fruits. The ADH activity of RG fruits was significantly lower than that of SG fruits at 30 DAP and the AAT activity was significantly lower than that of SG fruits at 42 DAP. In addition, the expression levels of CmADH and CmAAT homologs in RG fruits were significantly lower than those in SG or QG fruits. These results show that grafting with pumpkin rootstocks affected the main aroma components, reduced ADH and AAT activities, and down-regulated the expression levels of CmADHs and CmAATs in the melon fruits. This study reveals the mechanism of different rootstocks on melon fruit aroma quality, and lays a theoretical foundation for the selection of rootstocks in melon production. Future studies using overexpression or CRISPR/CAS system to obtain stable transgenic lines of genes encoding key aromatic volatiles, would be promising to effectively improve the flavor quality of melon.</p>
2023-11-21 | MTBLS8677 | MetaboLights