Lolium arundinaceum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA395224 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5853034_1.fastq.gz | Fastqsanger.gz | |||
| SRR5853034_2.fastq.gz | Fastqsanger.gz | |||
| SRR5853035_1.fastq.gz | Fastqsanger.gz | |||
| SRR5853035_2.fastq.gz | Fastqsanger.gz | |||
| SRR5853036_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: We aimed to dissect heat response of tall fescue and possible roles of melatonin and 24-epibrassinolide during thermotolerance. Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified genes modulated by short term heat (2h) and long term heat (12h) treatments.
2018-03-02 | GSE101699 | GEO
Project description:Fescue toxicosis affects wild and domestic animals consuming ergot alkaloids contained in tall fescue forage infected with the endophytic fungus, Neotyphodium coenophialum. , When animals are consuming infected fescue forage during periods of elevated ambient temperatures (summer), a range of phenotypic disorders collectively called summer slump is observed. It is characterized by hyperthermia, with an accompanying decrease in feed intake, growth, milk yield and reproductive fitness. Laboratory mice also exhibit symptoms of fescue toxicosis a thermoneutral temperature, as indicated by reduced growth rate and reproductive fitness. Our goal was to characterize the differences in gene expression in liver of mice exposed to summer-type heat stress (HS) and infected fescue (E+) when compared to mice fed infected fescue at thermoneutral temperature (TN). Mice were fed E+ diet under HS (34 ± 1°C; n = 13; E+HS) or thermoneutral (TN) conditions (24 ± 1°C; n = 14; E+TN) for a period of two weeks between 47 to 60 d of age. Genes differentially expressed between E+HS versus E+TN were identified using DNA microarrays. Forty-one genes were differentially expressed between treatment groups. Expressions of eight genes were measured using quantitative real-time PCR. Genes coding for phase I detoxification enzymes were up-regulated in E+HS mouse liver. This detoxification pathway is known to produce reactive oxidative species. We observed an up-regulation of genes involved in the protection against reactive oxidative species. Key genes involved in de novo lipogenesis and lipid transport were also up-regulated. Finally, genes involved in DNA damage control and unfolded protein responses were down-regulated. Keywords: Stress response
2006-08-29 | GSE5642 | GEO
Project description:Transcriptome response of tall fescue and its fungal endophyte in different climate change scenarios
| PRJNA1091660 | ENA
Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on the clinical symptoms and laboratory analyses of blood, it was hypothesized that such affected cattle display liver-specific changes in the expression of gene transcripts that are associated with the metabolic enzymes and transporters critical for beef health and performance. Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects the liver gene expression profiles of growing beef steers. Nineteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 9) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 10) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water and an industry standard mineral-vitamin supplement. 88 days grazing on pasture. Approximately 2 g of tissue from the right lobe of the liver of each steer were collected for RNA extraction and microarray analysis.
2010-11-30 | E-GEOD-23894 | biostudies-arrayexpress
Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on clinical and biochemical blood analyte profiles, hepatic targeted gene and protein analyses, and hepatic transcriptomic profiling, microarray analysis using the WT Btau 4.0 Array (version 1.0, Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects pituitary gene expression profiles of growing beef steers. The specific overall hypothesis tested was that grazing high endophyte-infected pasture would alter the pituitary genomic expression profiles of the same growing steers, especially genes involved in production and secretion of prolactin, growth hormone, thyroid stimulating hormone, and adrenocorticotropic hormone. Sixteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 8) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 8) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water, an industry standard mineral-vitamin supplement, and grazed respective pastures for 89 to 105 days. Whole pituitaries were collected for RNA extraction and microarray analysis.
2014-10-23 | E-GEOD-62570 | biostudies-arrayexpress
Project description:Rhododendron is well known woody plant, as having high ornamental and economic values. Heat stress is one of the important environmental stresses that effects Rhododendron growth. Recently, melatonin was reported to alleviate abiotic stress in plants. However, the role of melatonin in Rhododendron is still unknown. In the present study, the effect of melatonin on Rhododendron under heat stress and the potential mechanism was investigated. Through morphological characterization and chlorophyll a fluorescence analysis, 200µM was selected for the best melatonin concentration to mitigate heat stress in Rhododendron. To reveal the mechanism of melatonin priming alleviating the heat stress, the photosynthesis indexes, Rubisco activity and ATP content were detected in 25 ℃, 35 ℃ and 40 ℃. The results showed that melatonin improves electron transport rate (ETR), PSII and PSI activity, Rubisco activity and ATP content under high temperature stress. Furthermore, transcriptome analysis showed that a significant enrichment of differentially expressed genes in the photosynthesis pathway, and most of genes in photosynthesis pathway displayed a more significantly slight down-regulation under high temperature stress in melatonin-treatment plants, compared with melatonin-free plants. We identified PGR5……Together, these results demonstrate that melatonin could promote the photosynthetic electron transport, improve the enzymes activities in Calvin cycle and the production of ATP, and thereby increase photosynthetic efficiency and CO2 assimilation capacity under heat stress, through regulating the expression of some key genes, such as PGR5…Therefore, melatonin application displayed great potential to cope with the heat stress in Rhododendron.
2024-09-30 | GSE214428 | GEO
Project description:Longissimus muscle samples were collected from lambs exposed in utero to mycotoxins (E-, endophyte-free tall fescue seed without ergot alkaloids or E+, endophyte-infected tall fescue seed containing ergot alkaloids) during mid-gestation (MID; E+/E-; N) or late-gestation (LATE; E-/E+; T) harvested at two developmental stages (FETAL, gestational d133) or (MKT, near maturity, 250 d of age). Muscle samples were examined to determine the impact of in utero mycotoxin exposure on skeletal muscle fiber hypertrophy and the miRNA transcriptome at FETAL and MKT.
2022-06-03 | GSE195597 | GEO