Cucumis sativus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA560324 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9992833_1.fastq.gz | Fastqsanger.gz | |||
| SRR9992833_2.fastq.gz | Fastqsanger.gz | |||
| SRR9992834_1.fastq.gz | Fastqsanger.gz | |||
| SRR9992834_2.fastq.gz | Fastqsanger.gz | |||
| SRR9992835_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Three cucumbers genome sequencing and assembly
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Project description:miRNAs and its target genes under drought treatment of cucumbers (PRJCA041581)
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Project description:Genotyping arrays are tools for high throughput genotyping, which is required in genome-wide association studies (GWAS). Since the first cucumber genome draft was reported, genetic maps were constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and other sequence-related amplified polymorphism (SRAP). In this study we developed the first cucumber genotyping array which consisted of 32,864 single nucleotide polymorphisms (SNPs). These markers cover the cucumber genome every 2.1Kb and have parents/F1 hybridizations as a training set. The training set was validated with Fludigm technology and had 98% concordance. The application of the genotyping array was illustrated by constructed a genetic map of 600 cM in length based on recombinant inbred lines (RIL) population of a 9930XGy14 cross of which compromise of 11564 SNPs. The markers collinearity between the genetic map and genome references of the two parents estimated as R2=0.97. Moreover, this comparison supports a translocation in the beginning of chromosome 5 that occurred in the lineage of 9930 and Gy14 as well as local variation in the recombination rate. We also used the array to investigate the local allele frequencies along the cucumber genome and found specific region with segregation distortions. We believe that the genotyping array together with the training set would be a powerful tool in applications such as quantitative-trait loci (QTL) analysis and GWAS.
2015-05-01 | GSE57294 | GEO
Project description:Transcriptome data of cucumber before and after root-knot nematode infection
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Project description:Transcriptome data of cucumber before and after root-knot nematode infection
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Project description:Transcriptome data of cucumber before and after root-knot nematode infection
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Project description:Viroids are pathogenic non-coding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including an interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes and transposable elements. Indeed, several genes connected to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
2024-07-15 | GSE249651 | GEO
Project description:Study of hydrotropism-related gene expression in cucumber roots exposed to different gravitational conditions
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Project description:Obesity is caused by lipid accumulation in adipose tissues inducing adipocyte dysfunction, characterized by insulin resistance, increased lipolysis, oxidative stress, and inflammation, leading to increased levels of adipokines. Herein the capacity of the subfractions (SFs) SF1, SF2, and SF3 from the Cucumis sativus aqueous fraction and their combinations (M) to control adipocyte dysfunction in vitro, in 3T3-L1 adipocytes was studied. Adipocytes, previously treated with dexamethasone or IL-1 to induce dysfunction, were incubated with different concentrations of the subfractions for 24 h. 2-deoxyglucose consumption and glycerol release were evaluated, and a surface model was constructed to determine the most effective SF concentrations to improve both parameters. Effective SF combinations were assessed in their capacity to control metabolic, pro-oxidative, and pro-inflammatory conditions. SF1, SF2 (40 μg/ml each) and SF3 (20 μg/ml) improved 2-deoxyglucose consumption by 87%, 57%, and 87%, respectively. SF1 and SF2 (5 μg/ml each) and SF3 (40 μg/mL) increased glycerol secretion by 10.6%, 18.9%, and 11.8%, respectively. Among five combinations tested, only M4 (SF1 40 μg/ml:SF2 60 μg/ml:SF3 30 μg/ml) and M5 (SF1 40 μg/ml:SF2 60 μg/mL:SF3 10 μg/ml) controlled effectively the metabolic, pro-oxidative, and proinflammatory conditions studied. Glycine, asparagine, and arginine were the main components in these SFs.
| S-EPMC6746747 | biostudies-literature
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression profiles of cucumber under short-term chilling stress. The goals of this study are to transcriptome analysis of cucumber leaves under chilling stress. Methods: mRNA profiles of seedlings exposed to an air temperature of 6°C in the absence of light at 0, 2, 6, and 12 h were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays. Results: A total of 55.7 million clean reads was generated. Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2113 DEGs was identified at three time points (2, 6, and 12 h). A total of 30 genes was detected at all time points. The number of DEGs increased with time. In total, 100 TFs from 22 families in three subsets were detected. And 19 kinase families were identified in three subsets. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of cucumber in response to chilling stress. Exposure to a low temperature induced genes involved in hormone regulation, lipid metabolism, and photosynthesis, including NAC, WRKY, AP2/ERF, ERD, MYB as well as zinc finger TFs and protein kinases such as receptor-like protein kinase, MAPK, and CDK. Most TFs were upregulated whereas CDKs were downregulated. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.
2018-08-20 | GSE111998 | GEO