Cucumber
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA437026 | ENA |
REPOSITORIES: ENA
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Project description:The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and a long vs. short photoperiod.
2018-07-31 | GSE117867 | GEO
Project description:PLETHORA transcription factors (PLTs) are master regulators of plant development. In Arabidopsis, loss of shoot meristematic PLTs leads to destabilised phyllotaxis, but whether these factors have similar functions in more distantly related species, is not known. Here, we investigated the role of PLTs in shaping cucumber shoot architecture. Through transcriptional analysis, we determined that two of the four homologs - CsPLT3/7 and CsPLT5 - are expressed in complementary domains in the shoot apex. In situ hybridisation showed that whereas CsPLT3/7 was expressed in the shoot apical meristem summit and leaf axils, CsPLT5 transcripts localised beneath the CsPLT3/7 domain and to the adaxial side of leaf primordia. Both transcription factors recognised an ANT-like consensus motif and bound to SAM organising genes in vitro. Using a panel of TILLING mutants of each of the four CsPLT homologs, we only identified strong phenotypic defects for Csplt3/7 mutants. The combination of Csplt1/2 and Csplt3/7 proved embryonic lethal. In young seedlings, loss of CsPLT3/7 caused absence of a shoot apical meristem, which regenerated de novo shoot from a flat shoot apex during subsequent seedling development. Mature Csplt3/7 shoots exhibited defects in internode length stabilisation, revealing both extremely short and long internodes, stem architecture, flower morphology, and axillary organ initiation. Moreover, phyllotactic patterns were slightly shifted from a spiral towards a distichous orientation. We thus provide the first evidence of a role for PLTs in shoot development outside of Arabidopsis.
2026-01-19 | GSE294326 | GEO
Project description:PLETHORA transcription factors (PLTs) are master regulators of plant development. In Arabidopsis, loss of shoot meristematic PLTs leads to destabilised phyllotaxis, but whether these factors have similar functions in more distantly related species, is not known. Here, we investigated the role of PLTs in shaping cucumber shoot architecture. Through transcriptional analysis, we determined that two of the four homologs - CsPLT3/7 and CsPLT5 - are expressed in complementary domains in the shoot apex. In situ hybridisation showed that whereas CsPLT3/7 was expressed in the shoot apical meristem summit and leaf axils, CsPLT5 transcripts localised beneath the CsPLT3/7 domain and to the adaxial side of leaf primordia. Both transcription factors recognised an ANT-like consensus motif and bound to SAM organising genes in vitro. Using a panel of TILLING mutants of each of the four CsPLT homologs, we only identified strong phenotypic defects for Csplt3/7 mutants. The combination of Csplt1/2 and Csplt3/7 proved embryonic lethal. In young seedlings, loss of CsPLT3/7 caused absence of a shoot apical meristem, which regenerated de novo shoot from a flat shoot apex during subsequent seedling development. Mature Csplt3/7 shoots exhibited defects in internode length stabilisation, revealing both extremely short and long internodes, stem architecture, flower morphology, and axillary organ initiation. Moreover, phyllotactic patterns were slightly shifted from a spiral towards a distichous orientation. We thus provide the first evidence of a role for PLTs in shoot development outside of Arabidopsis.
2026-01-19 | GSE294327 | GEO
Project description:Orchid Dendrobium Sonia (Sonia) has wide demand in floral market throughout the world due to its vibrant coloured flowers, flowering recurrence and dense inflorescence. Effects of different monochromatic light qualities (red, far-red, blue, white) on different developmental and growth responses such as seed gemination, shoot and root growth, chlorophyll and carotenoid accumulation were studied in Sonia. Asymbiotic seed germination was the highest under blue or white light (80%, p<0.001) and least under far-red (55%, p<0.001) suggesting that it could either be controlled by an exceptional novel function of Cryptochrome 1 or the blue wavelengths perceived by PHYA or PHYB in Sonia. All analyses were done in 6-months-old plants till 1 year of age. Shoot length increased significantly in white or red light (3.7-fold, 3.5-fold respectively) while was least under far-red (decreased by 1.6-fold) indicating the major regulatory role of PHYB for shoot growth. Root growth in red in Sonia was more similar to hypocotyl adventitious root (HAR) formation genetically considering PHYB transcript expression. We suggest that the root growth (HAR) under red in Sonia is partly attributed to PHYB, negatively regulated with HY5 transcription factor and positively associated with auxin biosynthesis and accumulation gene BABY BOOM (BBM2) and efflux carriers such as LIKE AUXIN RESISTANT 2 and 3 (LAX2, LAX3). Highest chlorophyll content under far-red and blue might be a hyper-response of SAR under FR light in Sonia. Taxonomic tree analysis finds Sonia closer to Phalenopsis and Dendrobium catenatum Lindl. The three phytochromes and one cryptochrome sequences which were similar to PHYA, B, C and CRY1 respectively. CRY1 was retrieved with one more isoform CRY1_X2, with all these sequences more similar to those of Oryza.sativa. Further study can clarify the indicating reason of a probable gene loss which is evident from the absence of any sequence similar to CRY2 in root RNA isolates of Dendrobium Sonia.
2024-03-01 | GSE252123 | GEO
Project description:Shoot branching is an important agronomic trait that directly determines plant architecture and affects crop productivity. To promote crop yield and quality, axillary branches need to be manually removed during cucumber production for fresh market and thus are undesirable. Auxin is well known as the primary signal imposing for apical dominance and acts as a repressor for branching outside of the lateral buds. The TEOSINTE BRANCHED1/CYCLOIDEA /PCF (TCP) family gene BRANCHED1 (BRC1) has been shown to be the central integrator for multiple environmental and developmental factors that functions locally to inhibit shoot branching. However, no direct link has been reported between auxin and BRC1. Here, we find that cucumber BRANCHED1 (CsBRC1) is expressed in the axillary buds and displays higher expression level in cultivated cucumber than its wild ancestor. Knockdown of CsBRC1 by RNAi leads to increased bud outgrowth and reduced auxin accumulation in buds. We further show that CsBRC1 directly binds to two auxin efflux carriers PIN-FORMED (CsPIN1b and CsPIN3) and negatively regulates their expression. Ectopic expression of CsPIN1b or CsPIN3 driven by CsBRC1 promoter results in increased shoot branching. Moreover, shade induces the expression of CsBRC1 in cultivated cucumber, but not in wild ancestor, which may be partly due to the addition of two light response elements in the CsBRC1 promoter of cultivated cucumber. Therefore, our data suggest the formation of a regulatory pathway of shade-CsBRC1-auxin transport in suppressing lateral bud outgrowth during cucumber domestication.
2020-04-13 | GSE123949 | GEO
Project description:<p>The uptake and accumulation of nanoplastics by plants have raised particular concerns. However, molecular mechanisms underlying nanoplastic phytotoxicity are still vague and insufficient. Thus, its potential environmental risks and biosafety are receiving increased attention. In this study, cucumber plants were exposed to polystyrene nanoplastics (PSNPs) under different concentration. The results demonstrated that phenotypic parameters (total photosynthetic pigment content, relative membrane permeability, total phenolic content, and lipid peroxidation) were not significantly affected. However, metabolomic and transcriptomic analysis revealed that both doses of PSNPs induced the expression regulation of different key genes, exhibiting considerable distinction on metabolic responses in cucumber. The high dose of PSNPs induced stronger alteration in cucumber leaves than low dose of PSNPs. Low dose exposure significantly affected four metabolic pathways involved in the carbohydrate metabolism. High dose exposure significantly affected five metabolic pathways involved in the carbohydrate metabolism and four metabolic pathways involved in the amino acid metabolism. These findings shed new light on the phytotoxic mechanism and environmental implication behind the interaction of nanoplastics and plants, and advance our understanding of the potential adverse effect induced by the presence of nanoplastics in agricultural systems.</p>
2024-09-27 | MTBLS3923 | MetaboLights
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:Light intensity and spectral quality are two important factors that affect the cryopreservation success of plant germplasm. In a previous study, we found that LEDs with 90% red and 10% blue (RB) light have a positive effect on potato (Solanum tuberosum L.) shoot tip recovery during post-cryopreservation regeneration. In the present study, transcriptome profiles of non-cryopreserved (-) and cryopreserved (+) potato shoot tips exposed to RB, cool white fluorescent tubes (CW) and full darkness (D) were compared. Results indicated that light spectrum significantly affects transcript numbers in post-cryopreserved samples resulting in 3,284 differentially expressed genes of recovering shoot tips exposed to CW, RB and D. Gene ontology (GO) enrichment analysis revealed that several stress-related terms were more abundant in CW+, whereas morphogenesis-related processes were activated under RB+. Overall, cryopreservation had an extensive effect on gene expression, as 12,017 genes were differentially expressed in non-cryopreserved and cryopreserved shoot tips. Among all cryopreserved samples, enriched GO terms included various defense and stress responses to biotic stimuli and oxidative stress, whereas suppressed responses were mainly related to organ morphogenesis. The present study emphasizes that the optimization of light spectral properties to decrease light-related stress may greatly benefit the cryopreservation efficiency of plant germplasm.
2025-08-19 | GSE262492 | GEO
Project description:Background. Ovary culture has been a useful way to generate double haploid (DH) plant in cucumber (Cucumis sativus L.). However, the rate of embryo induction and the ability for induced embryo to grow into normal embryo are quite low. Moreover, the s mechanism of cucumber embryogenesis remains ambiguous. In this study, the molecular basis for cucumber embryogenesis was explored to set up basis for a more efficient ovary culture method. Differentially expressed genes during embryogenesis process, including the early stages of embryo formation, embryo maturation and shoot formation, were investigated using transcriptomic sequencing. Methods. Based on the cytological observation of cucumber ovary culture, the ovary culture can be divided into three stages:early embryo development, embryo maturation (from pre-embryos to cotyledon embryos) and the shoot formation stage. six key time points were selected for transcriptome sequencing and analysis. Results. We firstly conducted cytological observations which suggest that cell enlargement is the symbol for gametophytes to switch to sporophyte development pathway during early embryogenesis stage. In this stage, RNA-seq revealed 3468 up-regulated genes, including hormone signal transduction genes, hormone response genes and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. The total 480 genes that function in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the embryo maturation stage, indicating that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification during embryo development. In shoot formation stage, 1383 genes were up-regulated, which were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. The shoot formation stage might be regulated by 6 transcription factors that contained a B3 domain, 9 genes in the AP2/ERF family and 2 genes encoded WUS homologous domain proteins. Conclusions. These findings offer a valuable framework for explaining the transcriptional regulatory mechanism underlying embryogenesis during cucumber ovary culture.
2020-03-30 | GSE147282 | GEO
Project description:Polyamines play a pivotal role in plant growth and development by modulating metabolite levels and even regulating DNA methylation. To reveal novel insights into the intricate relationship among polyamines, metabolites and DNA methylation, the impact of exogenous putrescine on wheat was investigated at several levels. Since the outcome of putrescine treatment may vary depending on the light quality, the experiment was performed under both white and blue light. Metabolite profiling revealed distinct changes induced by blue light and/or putrescine. Blue light alone had increasing effects on several metabolites, but the effect of putrescine was dominant under blue light in most cases. Putrescine had a decreasing effect on some amino acids and the γ-glutamyl-cycle, while increasing effect on the TCA-cycle. Distinct changes in DNA methylation patterns were detected in response to blue light, putrescine or their combination. Blue light exerted strong effects on methylation, and putrescine application slightly could induce further changes. Putrescine had a higher impact under white as increased the leaf spermidine level, and parallel with this, a lower level of up-methylated genes involved in cellular processes, but a higher level of down-methylated genes involved in molecular function and biological processes occurred compared to the blue light.
2025-07-09 | GSE292105 | GEO