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Triticum aestivum

ABSTRACT: wheat AADD re-sequencing and RNA-Seq

PROVIDER: PRJNA608801 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11210500_1.fastq.gz	Fastqsanger.gz
	SRR11210500_2.fastq.gz	Fastqsanger.gz
	SRR11210501_1.fastq.gz	Fastqsanger.gz
	SRR11210501_2.fastq.gz	Fastqsanger.gz
	SRR11210502_1.fastq.gz	Fastqsanger.gz

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Triticum aestivum

Project description:wheat re-sequencing and RNA-seq

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Triticum aestivum Transcriptome or Gene expression

Project description:Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq). Note: All samples in SRA were assigned the same sample accession (SRS417803). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

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Wheat (Triticum aestivum L.) transcriptome profiling

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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [WES]

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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.

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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [RNA-seq]

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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.

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