Ontology highlight
ABSTRACT:
PROVIDER: PRJNA658445 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12489540_1.fastq.gz | Fastqsanger.gz | |||
| SRR12489540_2.fastq.gz | Fastqsanger.gz | |||
| SRR12489541_1.fastq.gz | Fastqsanger.gz | |||
| SRR12489541_2.fastq.gz | Fastqsanger.gz | |||
| SRR12489542.fastq.gz | Fastqsanger.gz |
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Project description:Oomycetes, such as the broad host-range necrotrophic plant pathogen Pythium myriotylum, cause devastating crop losses. We have previously identified P. myriotylum as the major pathogen infecting ginger (Zingiber officinale) rhizomes in China with symptoms of Pythium soft rot (PSR) disease. Ginger is an important crop with global production estimated at approximately three million metric tonnes with about 20% of this production in China. To better understand how P. myriotylum infects ginger, transcriptomic analysis was performed on two P. myriotylum isolates (SWQ7 and SL2) infecting ginger leaves. From both of the isolates, there was a clear separation between the transcriptome replicates from the mycelial control condition and those from the infection of the ginger leaf. In SWQ7 and SL2, there were 2,110 and 2,513 genes upregulated during infection of ginger, respectively. Of the putative effectors, a subset of the NEP1-like toxin protein (NLP) effectors were highly induced during the infection of ginger leaves. Insights from the transcriptome highlight the important role of a subset of plant cell wall degrading enzymes (PCWDEs) and effectors in the pathogenicity of P. myriotylum towards ginger. The surprisingly large numbers of P. myriotylum PCWDEs and effectors within the genome may be due to the broad host-range of P. myriotylum whereby particular subsets of the PCWDEs and effectors are required for pathogenicity towards particular hosts.
2022-07-22 | GSE174557 | GEO
Project description:Rhizome, root and leaf of Yellow ginger were compared in this study. Rhizomes from 2, 3, 4, 6, and 7 month old plants (after planting) were compared to each other and to root from 2 and 7 month plants and leaves from 2 and 7 month old plants. Plants were grown under controlled conditions in the greenhouse.
2009-07-09 | GSE16734 | GEO
Project description:Comparative analysis of micro-RNA (miRNA) in ginger-derived nanoparticles and ginger donor tissue using next-generation sequencing (NGS). The ginger-derived nanoparticles were prepared by differential ultracentrifuges. We mapped about 30 to 50 million sequence reads to the plant miRNA database and identified total of 2228 miRNAs including 532 miRNAs higher in nanoparticles and 1,280 miRNAs higner in tissue.
2021-05-19 | GSE153126 | GEO
Project description:Colitis is the common pathological lesion of inflammatory bowel diseases, the major chronic inflammatory diseases of intestinal tracts in humans. In this study, we investigated the therapeutic effects of ginger extract and its component zingerone in mice with 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis. Mice were administered with TNBS and/or various amounts of ginger and zingerone by an intrarectal route. The severity of colitis was evaluated by colonic weight/length ratio, macroscopic lesion, and histological examination. The mechanisms of ginger and zingerone were further elucidated by DNA microarray, ex vivo imaging, and immunohistochemical staining. Our data showed that treatment with ginger extract and zingerone ameliorated TNBS-induced colonic inflammation and injury in a dose-dependent manner. Pathway analysis of ginger- and zingerone-regulated gene expression profiles showed that ginger and zingerone significantly regulated cytokine-related pathways. Network analysis showed that nuclear factor-κB (NF-κB) and interleukin-1β (IL-1β) were key molecules involved in the expression of ginger- and zingerone-affected genes. Ex vivo imaging and immunohistochemical staining further verified that ginger and zingerone suppressed TNBS-induced NF-κB activation and decreased the NF-κB and IL-1β protein levels in the colon. In conclusion, our data showed that ginger improved the TNBS-induced colitis in mice via modulation of NF-κB activity and IL-1β signaling pathway. Moreover, zingerone might be the active component of ginger responsible for the amelioration of colitis induced by TNBS. A total of 24 mice was randomly divided into four groups of six mice: mock, mice were given with 0.1 ml of 50% ethanol; TNBS, mice were given with 250 mg/kg TNBS in 0.1 ml of 50% ethanol; TNBS/ginger, mice were administered with mixtures containing 250 mg/kg TNBS and various amounts of ginger extract in 0.1 ml of 50% ethanol; TNBS/zingerone, mice were given with mixtures containing 250 mg/kg TNBS and various amounts of zingerone in 0.1 ml of 50% ethanol. Mice were sacrificed seven days later for histochemical staining, RNA extraction, and ex vivo imaging.
2015-04-28 | E-GEOD-37677 | biostudies-arrayexpress
Project description:Colitis is the common pathological lesion of inflammatory bowel diseases, the major chronic inflammatory diseases of intestinal tracts in humans. In this study, we investigated the therapeutic effects of ginger extract and its component zingerone in mice with 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis. Mice were administered with TNBS and/or various amounts of ginger and zingerone by an intrarectal route. The severity of colitis was evaluated by colonic weight/length ratio, macroscopic lesion, and histological examination. The mechanisms of ginger and zingerone were further elucidated by DNA microarray, ex vivo imaging, and immunohistochemical staining. Our data showed that treatment with ginger extract and zingerone ameliorated TNBS-induced colonic inflammation and injury in a dose-dependent manner. Pathway analysis of ginger- and zingerone-regulated gene expression profiles showed that ginger and zingerone significantly regulated cytokine-related pathways. Network analysis showed that nuclear factor-κB (NF-κB) and interleukin-1β (IL-1β) were key molecules involved in the expression of ginger- and zingerone-affected genes. Ex vivo imaging and immunohistochemical staining further verified that ginger and zingerone suppressed TNBS-induced NF-κB activation and decreased the NF-κB and IL-1β protein levels in the colon. In conclusion, our data showed that ginger improved the TNBS-induced colitis in mice via modulation of NF-κB activity and IL-1β signaling pathway. Moreover, zingerone might be the active component of ginger responsible for the amelioration of colitis induced by TNBS.
2015-04-28 | GSE37677 | GEO
Project description:The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycetes-caused diseases such as Pythium myriotylum-caused rhizome rot in ginger leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using N. benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass content. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones, and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stress and the mechanisms of action of P. oligandrum as a biocontrol agent.
2023-06-22 | GSE235182 | GEO
Project description:Rhizome, root and leaf of Yellow ginger were compared in this study. Rhizomes from 2, 3, 4, 6, and 7 month old plants (after planting) were compared to each other and to root from 2 and 7 month plants and leaves from 2 and 7 month old plants. Plants were grown under controlled conditions in the greenhouse. We used an interwoven loop design for hybridizations. There are two interwoven loops included in this experiment: one for rhizome developmental stages (2, 3, 4, 6, and 7 months old), the other one for all tissues of 2 and 7 month old plants. These interwoven designs are connected at the 2 month old and 7 month old rhizome samples.
2010-05-16 | E-GEOD-16734 | biostudies-arrayexpress