Ontology highlight
ABSTRACT:
PROVIDER: PRJNA972543 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24564242_1.fastq.gz | Fastqsanger.gz | |||
| SRR24564242_2.fastq.gz | Fastqsanger.gz | |||
| SRR24564243_1.fastq.gz | Fastqsanger.gz | |||
| SRR24564243_2.fastq.gz | Fastqsanger.gz | |||
| SRR24564244_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study was to evaluate the physiological response and the expression analysis of `Dusa´ avocado rootstocks subjected to two different levels of water stress, and their subsequent recovery. At the beginning of the experiment, avocado plants were divided in Control plants (watered to field capacity (Fc) throughout the experiment) and stressed plants that were subjected to controlled substrate drying-up until they reached 50% of Fc (mild-WS) and 25% of Fc (severe-WS), respectively. Afterwards, plants were fully irrigated to assess drought recovery response. A set of physiological measurement were taken at leaf and whole-plant levels to assess avocado response to each level of water stress and rewatering. Root samples were collected in mild-WS and severe-WS and gene expression analysis was carried out using a targeted cDNA avocado stress microarray containing transcripts from de novo sequencing of 'Dusa' in response to biotic and abiotic stress. Avocado gene expression profiles under different levels of water stress are discussed in order to shed light on the molecular mechanisms associated with water deprivation in Dusa avocado rootstocks.
2021-11-03 | GSE151051 | GEO
Project description:Embryogenic cultures derived from a zygotic embryo of the avocado cv. Anaheim, were selected for resistance to the culture filtrate (CF) of Rosellinia necatrix, the causal agent of avocado white root rot. Cultures were obtained through recurrent selections in progressively increasing concentrations of fungal CF (from 20% up to 80%).
2023-09-01 | GSE228295 | GEO
Project description:PIWI proteins and their bound piRNAs form the core of a gonad specific small RNA silencing pathway in animals that protects the genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology, where TUDOR domains of various proteins recognize and bind symmetrically methylated Arginine residues in PIWI proteins. We systematically analyzed the Drosophila TUDOR protein family and identified three previously not characterized TUDOR domain-containing genes (CG4771, CG14303 and CG11133) as essential piRNA pathway members. We characterized CG4771 (Avocado) in detail and demonstrate a critical role for this protein during primary piRNA biogenesis in somatic and germline cells of the ovary. Avocado physically and/or genetically interacts with the primary pathway components Piwi, Armitage, Yb and Zucchini. Avocado also interacts with the Tdrd12 orthologs CG11133 and CG31755, which are essential for primary piRNA biogenesis in the germline and probably functionally replace the related and soma specific factor Yb.
2011-08-16 | GSE30955 | GEO
Project description:PIWI proteins and their bound piRNAs form the core of a gonad specific small RNA silencing pathway in animals that protects the genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology, where TUDOR domains of various proteins recognize and bind symmetrically methylated Arginine residues in PIWI proteins. We systematically analyzed the Drosophila TUDOR protein family and identified three previously not characterized TUDOR domain-containing genes (CG4771, CG14303 and CG11133) as essential piRNA pathway members. We characterized CG4771 (Avocado) in detail and demonstrate a critical role for this protein during primary piRNA biogenesis in somatic and germline cells of the ovary. Avocado physically and/or genetically interacts with the primary pathway components Piwi, Armitage, Yb and Zucchini. Avocado also interacts with the Tdrd12 orthologs CG11133 and CG31755, which are essential for primary piRNA biogenesis in the germline and probably functionally replace the related and soma specific factor Yb. small RNA libraries were prepared from total RNA isolation of 8 different genotypes
2011-08-16 | E-GEOD-30955 | biostudies-arrayexpress
Project description:Background: Rosellinia necatrix is the causal agent of avocado white root rot (WRR). Control of this soil-borne disease is difficult and tolerant rootstocks may represent an effective method to lessen its impact. To date, no studies on molecular mechanisms regulating the avocado plant response towards this pathogen have been undertaken. To shed light onto the mechanisms underpinning disease susceptibility and tolerance, molecular analysis of the gene's response of two contrasting-disease-reaction avocado rootstocks was assessed. Results: Gene expression profiles against R. necatrix were assessed in the susceptible 'Dusa' and the tolerant selection BG83 avocado genotypes by micro-array analysis. In 'Dusa', the early response is mainly related to redox processes and cell-wall degradation activities, all becoming more remarkable after disease progression affected photosynthetic capacity; whereas, tolerance to R. necatrix in BG83 relies on the induction of protease inhibitors and their negative regulators, as well as salt and osmotic stress related genes besides oxido-reduction processes. We identified three protease inhibitors, glu protease, trypsin and endopeptidase inhibitors, highly overexpressed in the tolerant genotype, when compared to susceptible 'Dusa', after infection with R. necatrix, reaching fold change values of 44, 34 and 16 respectively. Conclusions: The contrasting results between 'Dusa' and BG83 give new insights into the different mechanisms involved in the avocado tolerance to P. cinnamomi and R. necatrix, which are consistent with their biotrophic and necrotrophic lifestyles, respectively. The differential induction of genes involved in salt and osmotic stress in BG83 could indicate that R. necatrix penetration into the roots is associated with osmotic effects suggesting that BG83's tolerance to R. necatrix is related to the ability to withstand osmotic imbalance. In addition, the high expression of protease inhibitors in tolerant BG83 compared to susceptible 'Dusa' after infection with the pathogen, suggests the important role that these proteins could play in the defence of avocado rootstocks against R. necatrix.
2019-02-26 | GSE119140 | GEO
Project description:We explore whether a low-energy diet intervention for Metabolic dysfunction-associated steatohepatitis (MASH) improves liver disease by means of modulating the gut microbiome. 16 individuals were given a low-energy diet (880 kcal, consisting of bars, soups, and shakes) for 12 weeks, followed by a stepped re-introduction to whole for an additional 12 weeks. Stool samples were obtained at 0, 12, and 24 weeks for microbiome analysis. Fecal microbiome were measured using 16S rRNA gene sequencing. Positive control (Zymo DNA standard D6305) and negative control (PBS extraction) were included in the sequencing. We found that low-energy diet improved MASH disease without lasting alterations to the gut microbiome.
2024-12-31 | E-MTAB-14061 | biostudies-arrayexpress
Project description:Phytophthora cinnamomi Rands (Pc) is a hemibiotrophic oomycete and the causal agent of Phytophthora root rot (PRR) of the commercially important fruit crop avocado (Persea americana Mill.). Plant defense against pathogens is modulated by phytohormone signaling pathways such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET), auxin and abscisic acid. The role of specific signaling pathways induced and regulated during hemibiotroph-plant interactions has been widely debated. Some studies report SA mediated defense while others hypothesize that JA responses restrict the spread of pathogens. This study aimed to identify the role of SA- and JA- associated genes in the defense strategy of a resistant avocado rootstock, Dusa® in response to Pc infection. Transcripts associated with SA-mediated defense pathways and lignin biosynthesis were upregulated at 6 hours post-inoculation (hpi). Results suggest that auxin, reactive oxygen species (ROS) and Ca2+ signaling was also important during this early time point, while JA signaling was absent. Both SA and JA defense responses were shown to play a role during defense at 18 hpi. Induction of genes associated with ROS detoxification and cell wall digestion (β-1-3-glucanase) was also observed. Most genes induced at 24 hpi were linked to JA responses. Other processes at play in avocado at 24 hpi include cell wall strengthening, the formation of phenolics and induction of arabinogalactan, a gene linked to Pc zoospore immobility. This study represents the first transcriptome wide analysis of a resistant avocado rootstock treated with SA and JA compared to Pc infection. The results provide evidence of a biphasic defense response against the hemibiotroph, which initially involves SA-mediated gene expression followed by the enrichment of JA-mediated defense from 18 to 24 hpi. Genes and molecular pathways linked to Pc resistance are highlighted and may serve as future targets for manipulation in the development of PRR resistant avocado rootstocks.
2018-11-14 | GSE119635 | GEO