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Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs

ABSTRACT: Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs

PROVIDER: PRJNA339474 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4044040.fastq.gz	Fastqsanger.gz
	SRR4044035.fastq.gz	Fastqsanger.gz
	SRR4044036.fastq.gz	Fastqsanger.gz
	SRR4044037.fastq.gz	Fastqsanger.gz
	SRR4044038.fastq.gz	Fastqsanger.gz

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Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs [PARE]

Project description:RNA interference (RNAi) is a conserved, RNA-mediated, regulatory mechanism in eukaryotes. In plants, it plays an important role in growth, development and resistance against viral infections. As a counter-defence, plant viruses, e.g. geminiviruses, encode RNAi suppressors, such as AC2, AC4 and AV2. To obtain Nicotiana tabacum virus resistant plants against Tomato leaf curl New Delhi virus (ToLCNDV), we employ the biogenesis pathway of a class of endogenous siRNAs, the trans-acting siRNAs (ta-siRNAs), by engineering artificial ta-siRNAs (ata-siRNAs) targeting the AC2 (TRiV-AC2) and AC4 (TRiV-AC4) RNAi suppressors using miRNA390 dual target sites. The mode of action of ta-siRNAs comprises of the cleavage of the target (similar to the miRNA targeting). Using degradome approaches, the abundance of the resulting 3' fragment of the cleaved transcript can be quantified and the precise localization of the cleavage on the target mRNA can be identified. We sequenced degradome libraries of Nicotiana tabacum plants infected with ToLCNDV which were treated with the ata-siRNA-AC2 construct; mock-treated plants were used as controls. Following quality checks, the abundance distributions of the degradation fragments were normalized. The transcripts with different cleavage patterns was the AC2, supporting the conclusion that an efficient cleavage of the target occurred, without significant off-target effects.

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Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs [sRNA-seq]

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Project description:Tomato leaf curl New Delhi virus Genome sequencing

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Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs

Project description:This SuperSeries is composed of the SubSeries listed below.

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Tomato leaf curl New Delhi virus (ToLCNDV)

Project description:Tomato leaf curl New Delhi virus (ToLCNDV) ssDNA plant begomovirus (Family geminiviridae) isolated from Potato in Pakistan.

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An improved protocol for small RNA library construction by using High-Definition adapters

Project description:Most of small RNA library construction methods are based on RNA ligases, which prefer to join the molecules (small RNAs and adapters) that can anneal to each other and form a ligase favoured structure. Different platforms for next generation sequencing use different adapter sequences, causing the cloning bias. Adapters with degenerated nucleotides at the ligating ends (High Definition, HD adapters) were developed to reduce the cloning bias. However, above 90% of the cloning products is adapter dimer when the current available commercial kits and their corresponding protocols are used. Here we adopted and further improved a method demonstrated in a publically available patent (http://www.google.com/patents/WO2011056866A2?cl=en). Using the improved method, we constructed the small RNA libraries by using the total RNA of Medicago truncatula leaf tissue. The adapter dimer was significantly reduced. The small RNA sequences were also analysed.

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