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ABSTRACT: Transcriptome analysis of Nicotiana tabacum infected by Tomato leaf curl Gujarat virus

PROVIDER: PRJNA787909 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17194537_1.fastq.gz	Fastqsanger.gz
	SRR17194537_2.fastq.gz	Fastqsanger.gz
	SRR17194538_1.fastq.gz	Fastqsanger.gz
	SRR17194538_2.fastq.gz	Fastqsanger.gz
	SRR17194539_1.fastq.gz	Fastqsanger.gz

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Nicotiana tabacum

Project description:Transcriptome analysis of Nicotiana tabacum infected by Tomato leaf curl Gujarat virus

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Transcriptomic analysis of tomato plants infected by the geminivirus TYLCSV

Project description:Gene expression of tomato plants infected by Tomato yellow leaf curl Sardinia virus (TYLCSV) and mock inoculated were compared.

2014-02-01 | E-MEXP-3953 | biostudies-arrayexpress

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.

2019-11-08 | GSE85818 | GEO

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]

2019-11-08 | GSE85816 | GEO

Characterization of small interfering RNAs derived from the geminivirus/betasatellite complex using deep sequencing

Project description:Small RNA (sRNA)-guided RNA silencing is a critical antiviral defense mechanism employed by a variety of eukaryotic organisms. Although the induction of RNA silencing by bipartite and monopartite begomoviruses has been described in plants, the nature of begomovirus/betasatellite complexes remains undefined. We profiled Tomato yellow leaf curl China virus (TYLCCNV) and its associated betasatellite (TYLCCNB)-derived small RNAs (V-sRNAs and S-sRNAs) using Solexa-based deep sequencing to evaluate the role of betasatellites in V-sRNA modulation. Both sense and anti-sense V-sRNAs and S-sRNAs accumulated preferentially as 22 nucleotide species in infected Solanum lycopersicum and Nicotiana benthamiana plants, indicating that secondary siRNAs were triggered. High resolution mapping of V-sRNA and S-sRNA revealed heterogeneous distribution of V-sRNA and S-sRNA sequences across the TYLCCNV and TYLCCNB genomes. In TYLCCNV-infected S. lycopersicum or N. benthamiana and TYLCCNV and betaC1-mutant TYLCCNB co-infected N. benthamiana plants, the primary TYLCCNV targets were AV2 and the 5’ terminus of AV1. In TYLCCNV and betasatellite-infected plants, the number of V-sRNAs targeting this region decreased and the production of V-sRNAs increased corresponding to the overlapping regions of AC2 and AC3, as well as the 3’ terminal of AC1. betaC1 is the primary determinant mediating symptom induction and also the primary silencing target of the TYLCCNB genome even in its mutated form. In addition, the betasatellite affected the amount of V-sRNAs detected in S. lycopersicum and N. benthamiana plants. characterization of Tomato yellow leaf curl China virus and Tomato yellow leaf curl China betasatellite-derived small interfering RNAs from five cDNA libraries of two plant species

2011-08-21 | E-GEOD-26368 | biostudies-arrayexpress

Geminiviruses employ host DNA glycosylases to subvert DNA methylation-mediated defense

Project description:DNA methylation is an epigenetic mechanism that plays important roles in gene regulation and transposon silencing. Active DNA demethylation has evolved to counterbalance DNA methylation at many endogenous loci. Here, we report that active DNA demethylation also targets viral DNAs, tomato yellow leaf curl China virus (TYLCCNV) and its satellite tomato yellow leaf curl China betasatellite (TYLCCNB), to promote their virulence. We demonstrate that the βC1 protein, encoded by TYLCCNB, interacts with a ROS1-like DNA glycosylase in Nicotiana benthamiana and with the DEMETER (DME) DNA glycosylase in Arabidopsis thaliana. The interaction between βC1 and DME facilitates the DNA glycosylase activity to decrease viral DNA methylation and promote viral virulence. These findings reveal that active DNA demethylation can be regulated by a viral protein to subvert DNA methylation-mediated defense.

2021-12-20 | GSE188968 | GEO

Expression data in response to pepper leaf curl virus (PepLCV) infection in Chili pepper at three leaf stage

2012-10-11 | GSE41131 | GEO

Expression data in response to pepper leaf curl virus (PepLCV) infection in Chilli pepper at three leaf stage

Project description:A comparative study to determine the pepper leaf curl virus resistance machanism between resistant and susceptible genotypes at three leaf stage. To study the molecular mechanism of pepper leaf curl virus (PepLCV) resistance, pepper plants were exposed to PepLCV through artificial inoculation and hybridization on Agilent tomato microarrays. The expression analysis of PepLCV resistant and susceptible genotypes after artificial inoculation at three leaf stage showed that the resistance against PepLCV is due to sum of expression of hundreds of genes at a particular stage. Tomato microarrays consisting of 43,803 probes were used for whole genome expression analysis of chilli peppers for resistance against PepLCV. Transcripts from the leaves of resistant (BS-35) and susceptible plants (IVPBC-535) were compared in response to PepLCV inoculation at three leaf stage.

2012-10-11 | E-GEOD-41131 | biostudies-arrayexpress

Identification of tomato proteins that interact with Replication initiator protein (Rep) of the geminivirus TYLCV

Project description:In this study, an GFP-based affinity purification followed by mass spectrometry (AP-MS) approach is used in order to identify new tomato proteins that interact with the Replication initiator protein (Rep, AL1, C1) from Tomato yellow leaf curl virus (TYLCV).

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Transcriptional reprogramming in transgenic Arabidopsis plants expressing C4G2A and a cas-1 mutant upon activation of plant immunity.

Project description:Transcriptional overlap between transgenic Arabidopsis plants expressing C4G2A from the Tomato yellow leaf curl virus (TYLCV) and a cas-1 mutant upon activation of plant immunity by treatment with the bacterial peptide elicitor flg22 (1 µM, 12 h).

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