Genome-wide Identification of Fusarium graminearum-Responsive lncRNAs in Triticum aestivum
Ontology highlight
ABSTRACT:
ORGANISM(S): Triticum aestivum
PROVIDER: GSE158213 | GEO | 2023/09/18
REPOSITORIES: GEO
Similar Datasets
Project description:Triticum aestivum cv. fielder infected with Fusarium graminearum raw sequence reads
| PRJNA307989 | ENA
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived Triticum aestivum transcriptome (RNA-seq) profiling methods and to evaluate genotypes associated with resistance against the Wheat dwarf virus. Methods: Triticum aestivum mRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated by deep sequencing, in four replicates, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our study represents the first detailed analysis of Triticum aestivum transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA and miRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-04-04 | GSE192518 | GEO
Project description:Fusarium graminearum (F.g) is responsible for Fusarium head blight (FHB), which is a destructive disease of wheat that accumulates mycotoxin such as deoxynivalenol (DON) and makes its quality unsuitable for end use. Several FHB resistant varieties development is going on world-wide. However the complete understanding of wheat defence response, pathogen (Fusarium graminearum) disease development mechanism and the gene crosstalk between organisms is still unclear. In our study focused to analyse pathogen (F. graminearum) molecular action in different Fusarium head blight resistance cultivars during the disease development. To understand the Fusarium graminearum pathogen molecular reaction, microarray gene expression analysis was carried out by using Fusarium graminearum (8 x 15k) Agilent arrays at two time points (3 & 7 days after infection) on three wheat genotypes (Japanese landrace cv. Nobeokabouzu-komugi - highly resistant, Chinese cv. Sumai 3 - resistant and Australian cv. Gamenya - susceptible), which spikes infected by Fusarium graminearum ‘H-3’strain. During the disease development the pathogen biomass as well as the expression of Trichothecene biosynthesis involved genes (Tri genes) in three wheat cultivars was determined. In our material no relation between fungus biomass and the disease symptoms were observed, however, it showed relation with fungus virulence factors expression (Tri genes). For the first time, we report the nature of Fusarium graminearum gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease development stage and the possible underlying molecular response.
2015-03-14 | GSE66772 | GEO
Project description:MS2 data for two Indian varieties of Triticum aestivum L. (Wheat). P1 to P5 files represent MS2 data in positive ESI mode whereas N1 to N5 files represent MS2 data in negative ESI mode.
2023-04-23 | MSV000091783 | MassIVE
Project description:Wheat is the staple food of over 35% of the world’s population, accounts for 20% of all human calories, and its yield and quality improvement is a focus in the effort to meet new demands from population growth and changing diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome. With the aim of creating a resource complementary to current genome sequencing and assembly projects and to aid researchers in the specific analysis and measurement of wheat proteins of interest, we present a large scale, publicly accessible database of identified peptides and proteins derived from the proteome mapping of Triticum aestivum. This current dataset consists of twenty four organ and developmental samples in an online interactive resource allowing the selection, comparison and retrieval of proteomic data with rich biochemical annotation derived from multiple sources. Tissue specific sub-proteomes and ubiquitously expressed markers of the wheat proteome are identified alongside hierarchical assessment of protein functional classes and their presence in different tissues. The impact of wheat’s polyploid genome on proteome analysis and the effect on defining gene specific and protein family relationships is accounted for in the organisation of the data. The dataset will serve as a vehicle to build, refine and deposit confirmed targeted proteomic assays for wheat proteins and protein families to assess function.
2016-11-17 | PXD004720 | Pride
Project description:Salicylic acid (SA) is one of the key signal molecules in regulating plant resistance to diverse pathogens. It is predominantly associated with resistance against biotrophic and hemibiotrophic pathogens, and triggering systemic acquired resistance (SAR) in Arabidopsis. However, whether and how SA directly affects Fusarium graminearum and how SA influences the defence efficiency of wheat against fusarium head blight (FHB) are still poorly understood. Previous experiments have shown that the growth of F. graminearum mycelia and the germination of spores were significantly inhibited, and eventually stopped by increasing amounts of SA in both liquid and solid media cultures. Co-inoculation of SA and Fg spores has led to reduced FHB symptoms in the very susceptible Triticum aestivum cultivar ‘Roblin’. To better understand the effect of SA on F. graminearum mycelial growth, we have compared the expression profiles of SA-treated and untreated F. graminearum liquid cultures after 8 and 24 h of treatment, using an F. graminearum custom-commercial microarray. The microarray analysis suggests that F. graminearum can metabolize SA through two pathways, the gentisate and catechol pathways that are present in many fungal species. Additional experiments have confirmed the capacity of F. graminearum to metabolize SA. Our results demonstrate that, although F. graminearum has the capacity to metabolize SA, SA has a significant and direct impact on F. graminearum through a reduction in efficiency of germination and growth at higher concentrations.
2011-12-15 | GSE24636 | GEO
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Triticum aestivum tissues (including leaves and spiklets infected with Fusarium and control). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.
2011-09-30 | GSE32476 | GEO
Project description:Salicylic acid (SA) is one of the key signal molecules in regulating plant resistance to diverse pathogens. It is predominantly associated with resistance against biotrophic and hemibiotrophic pathogens, and triggering systemic acquired resistance (SAR) in Arabidopsis. However, whether and how SA directly affects Fusarium graminearum and how SA influences the defence efficiency of wheat against fusarium head blight (FHB) are still poorly understood. Previous experiments have shown that the growth of F. graminearum mycelia and the germination of spores were significantly inhibited, and eventually stopped by increasing amounts of SA in both liquid and solid media cultures. Co-inoculation of SA and Fg spores has led to reduced FHB symptoms in the very susceptible Triticum aestivum cultivar ‘Roblin’. To better understand the effect of SA on F. graminearum mycelial growth, we have compared the expression profiles of SA-treated and untreated F. graminearum liquid cultures after 8 and 24 h of treatment, using an F. graminearum custom-commercial microarray. The microarray analysis suggests that F. graminearum can metabolize SA through two pathways, the gentisate and catechol pathways that are present in many fungal species. Additional experiments have confirmed the capacity of F. graminearum to metabolize SA. Our results demonstrate that, although F. graminearum has the capacity to metabolize SA, SA has a significant and direct impact on F. graminearum through a reduction in efficiency of germination and growth at higher concentrations. Untreated and Salicylic Acid (SA) treated liquid cultures of F. graminearum at 8h and 24h collection times. Three biological replicates per time point and treatment, 2 technical replicates (dye flips) per sample.
2011-12-15 | E-GEOD-24636 | biostudies-arrayexpress