Cucumis sativus cultivar:JinYou 1
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ABSTRACT:
PROVIDER: PRJNA449125 | ENA |
REPOSITORIES: ENA
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Project description:Cucumis sativus Transcriptome sequencing to salt-stressed roots
| PRJNA511946 | ENA
Project description:Dodder transmits salt-induced systemic signals between cucumber hosts
| PRJNA524275 | ENA
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
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
| PRJNA707661 | ENA
Project description:Transcriptome data of cucumber before and after root-knot nematode infection
| PRJNA707668 | ENA
Project description:Transcriptome data of cucumber before and after root-knot nematode infection
| PRJNA707667 | ENA
Project description:Ethylene, as a signaling hormone molecule, is proved to have essential role in the process of root development. In the present study, cucumber (Cucumis sativus L.) seedlings were employed to estimate differentially expressed proteins (DEPs) during the adventitious rooting using iTRAQ technique and proteomics analysis. Out of the 5014 DEPs, 115 DEPs were considered as identified proteins, and among them, 24 DEPs are interesting proteins abundance.
2020-01-15 | PXD016444 | Pride
Project description:Nitrogen is the most important mineral nutrient of plant. As a worldwide and economically important vegetable, cucumber (Cucumis sativus L.) has a strong nitrogen-dependence. We took whole transcriptome sequencing approach to compare the gene expression profiles of cucumber leaves and roots grown under sufficient or insufficient nitrate supply. Analysis of the transcriptome data revealed that the root and leaf adapt different response mechanisms to long-term nitrogen deficiency. Photosynthesis and carbohydrate biosynthetic process were pronouncedly and specifically reduced in leaf, while the ion transport function, cell wall and phosphorus-deficiency response function seem systematically down-regulated in root. Genes in nitrogen uptake and assimilation are decreased in root, but some are increased in leaf under nitrogen deficiency. Several lines of evidence suggest that the altered gene expression networks support the basic cucumber growth and development likely through successful nitrogen remobilization involving in the induced expression of genes in ABA and ethylene pathways. cucumber leaf and root mRNA of 28-day after sowing nitrogen deficiency and sufficiency deep sequencing, using Illumina HiSeq 2000
2015-05-07 | E-GEOD-46678 | biostudies-arrayexpress
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109617 | GEO