Project description:Due to its small and sequenced genome, short generation time, efficient transformation and increasing genetic resources, Brachypodium distachyon is an emerging model for grasses. Despite this, data capturing gene expression patterns across different organs and developmental stages is missing. We have generated a comprehensive gene expression atlas for Brachypodium, capturing 9 different organs and developmental stages
Project description:In this study we treated Brachypodium distachyon roots with synthetic auxin, 2,4-D, to induce nodule-like structures (NLS) and performed RNA-seq to assess transcriptome changes during NLS formation. Overall design: Three biological replicates per treatment; total RNA was isolated individually from each replicate.
Project description:Deep sequencing of Brachypodium distachyon small RNA from panicles (flowers) was done to analyze the genome-wide distribution patterns of 1) total small RNA reads and loci, 2) 21 and 24 nucleotide repeat-normalized reads and 3) 21 and 24 nucleotide phased siRNA clusters relative to gene and transposable element density. Overall design: Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR. DNA amplicons were sequenced using an Ilumina Genome Analyzer. Resulting sequences were computationally trimmed to remove 3' adaptor sequences. Raw data for GSM506621 was not provided.
Project description:RNA-seq reads generated from Brachypodium distachyon (Bd21-3) seedlings infected with Fusarium pseudograminearum. Samples were collected 3 days post innoculation in four replicates.
Project description:The aim was to determine the changes in cell wall composition and transcriptome changes following treatment with the stress hormone precursor methyl jasmonate (MeJA) in the model grass Brachypodium distachyon. The correlation between transcript changes and cell wall composition changes allowed identification of candidate genes responsible for grass-specific features of the cell wall that are specifically changed in response to MeJA.
Project description:Plants are continuously exposed to varying environmental conditions; some anticipated diurnal changes in light and temperature and others far less predictable. Key to adaptation to a diurnal environment is the anticipation provided by the circadian clock, which coordinates broad changes in gene expression with a period of about 24 h.Here we present the analysis of RNA sequencing to measure transcript abundance over time in Brachypodium distachyon entrained in photo- and thermocycles then transferred to photocycles or thermocycles alone, or constant light and temperature conditions.
Project description:The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using Parallel Analysis of RNA Ends (PARE) data is lacking in B. distachyon. B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset to analyze small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants. Examination of various tissues and stresses in Brachypodium by high throughput sequencing for small RNA profiling and PARE (Parallel Analysis of RNA Ends)
Project description:affy_brachy_2011_11 - affy_brachy_2011_11 - Fusarium graminearum is the causal agent of Fusarium head blight (FHB) of small-grain cereals, including wheat. Besides direct grain losses, this disease is of major concern because of the production by the pathogen of mycotoxins which are hazardous to animals, thus making the grain unfit for food or feed. Major mycotoxins produced by the fungus are trichothecens, including deoxynivalenol (DON). In our laboratory, we use Brachypodium distachyon as a model plant for cereals because of its amenability (short life cycle, numerous genomic and genetic resources, ...). We have recently shown that F. graminearum does induce head blight symptoms on this species and that DON is produced on infected spikes. We have also evidenced that a F. graminearum strain unable to produce DON exhibits reduced virulence on B. distachyon spikes, as previously shown on wheat. The aim of this project is to analyse and compare the plant response to DON producing and non-producing strains of F. graminearum. This analysis will allow to decipher the mechanisms of detoxification set up by the plant and also more specific responses due to the impact of the mycotoxin on plant metabolism and physiology. -Three conditions on B. distachyon spikes: 1-Mock inoculation (Tween 20 0,01%) 2-Inoculation by a F. graminearum wild-type strain 3-Inoculation by a F. graminearum mutant strain, unable to produce DON Spikes were point inoculated with 3ul of either Tween 20 0.01%, wild-type strain or mutant strain (300 spores) and incubated for 96 hours. Six inoculated spikes were collected and pooled for each condition and biological replicate. Three independent biological replicates were conducted. 9 arrays - Brachypodium; normal vs disease comparison,time course
Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA Overall design: One wheat small RNA library (Tae) and two Brachypodium small RNA libraries (BdR and BdV) were sequenced.
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4400 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4400/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)