Triticum aestivum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA383677 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5464520.fastq.gz | Fastqsanger.gz | |||
| SRR5464523.fastq.gz | Fastqsanger.gz | |||
| SRR5464524.fastq.gz | Fastqsanger.gz | |||
| SRR5464515.fastq.gz | Fastqsanger.gz | |||
| SRR5464507.fastq.gz | Fastqsanger.gz |
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Project description:Whole-transcriptome sequencing of wheat (Triticum aestivum) Raw sequence reads
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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:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity.
2014-08-20 | GSE53487 | GEO
Project description:In present experiment we evaluated the effects of the utrasonication of winter wheat seeds on seedling growth and development. Effect of treatment on the gene transcription and DNA methylation of seedlings were evaluated.
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Project description:Transcriptome profiling of wheat caryopsis development
| PRJNA102407 | ENA
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:ChIP-seq Raw sequence reads of wheat and its ancestors
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Project description:The pistillody mutant wheat (Triticum aestivum L.) plant HTS-1 exhibits homeotic transformation of stamens into pistils or pistil-like structures. Unlike common wheat varieties, HTS-1 produces three to six pistils per floret, potentially increasing the yield. Thus, HTS-1 is highly valuable in the study of floral development in wheat. In this study, we conducted RNA sequencing of the transcriptomes of the pistillody stamen (PS) and the pistil (P) from HTS-1 plants, and the stamen (S) from the non-pistillody control variety Chinese Spring TP to gain insights into pistil and stamen development in wheat.
2014-03-14 | E-MTAB-4469 | biostudies-arrayexpress
Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity. Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx
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