Hordeum vulgare
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB16672 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR505018_1.fastq.gz | Fastqsanger.gz | |||
| DRR505018_2.fastq.gz | Fastqsanger.gz | |||
| DRR505019.fastq.gz | Fastqsanger.gz | |||
| DRR505020.fastq.gz | Fastqsanger.gz | |||
| DRR505021.fastq.gz | Fastqsanger.gz |
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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 different Hordeum vulgare tissues (leaves, inflorescence and leaves inoculated with Blumeria). 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 maize genome under study.
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Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates.
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Project description:A DNA microarray analysis detected large-scale changes of gene expression in response to Cd stress with a substantial difference between the two barley genotypes differing in Cd tolerance and accumulation. Cd stress led to higher expression of genes involved in transport, carbohydrate metabolism and signal transduction in the low-grain-Cd-accumulating genotype. Novel transporter genes such as zinc transporter genes were identified as being associated with low Cd accumulation. We used microarrays to understand the mechanism of low Cd accumulation in crops which is crucial for sustainable safe food production in Cd-contaminated soils.
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Project description:Transcription profiling of barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes
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Project description:BackgroundIn nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored.ResultsThis study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable.ConclusionsHere, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.
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Project description:Pathogenesis-related protein 1a of Hordeum vulgare subsp. Vulgare (HvPR-1a) is induced by various pathogens and stress related factors. It plays important roles in plant defense system. Since the discovery of HvPR-1a a great deal of research has been focused on its isolation and characterization. However, three dimensional structure of HvPR-1a is still unknown. 3D structure can be used for determining protein function, and identifying novel protein folds and potential targets for regulation. The protein model was developed using MODELLER 9v10. Physicochemical characterization and functional annotation of the model carried out with Expasy's ProtParam server and three different conserved domain finding programs including InterProScan, Proteins Families Database (Pfam), and NCBI Conserved Domains Database (NCBI-CDD). Applying validation programs revealed that the model has good quality and the RMSD value is 0.7. The predicted model submitted in Protein Model Database, PMDB for public use. This model will be used in wide range of studies for functional analysis and improvement activity of the protein.
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