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Arabidopsis thaliana

ABSTRACT: Tobacco mosaic virus infection alters phloem associated translatomes in Arabidopsis thaliana

PROVIDER: PRJNA382580 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5444360.fastq.gz	Fastqsanger.gz
	SRR5444361.fastq.gz	Fastqsanger.gz
	SRR5444362.fastq.gz	Fastqsanger.gz
	SRR5444363.fastq.gz	Fastqsanger.gz
	SRR5444354.fastq.gz	Fastqsanger.gz

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Tobacco mosaic virus infection alters phloem associated translatomes in Arabidopsis thaliana

Project description:In this study we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem-associated translatome responses to infection by tobacco mosaic virus (TMV) in the systemic host Arabidopsis thaliana ecotype Shahdara. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from the leaves of 5-week-old plants inoculated with TMV (1 mg/mL) or mock inoculated with sterile water.

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Project description:Tobacco mosaic virus infection alters phloem associated translatomes in Nicotiana benthamiana

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Phloem and non-phloem associated translatomes during plum pox virus infection in Prunus domestica L. II

Project description:In this study we used a translating ribosome affinity purification strategy to identify phloem and non-phloem associated translatomes in Prunus domesitca L during PPV infection. Three different promoter:His6FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from plum leaves taken at 2, 4, 6, and 12 weeks post cold induced dormancy.

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Phloem and non-phloem associated translatomes during plum pox virus infection in Prunus domestica L.

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Tobacco mosaic virus infection alters phloem associated translatomes in Nicotiana benthamiana

Project description:In this study we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem-associated translatome responses to infection by tobacco mosaic virus (TMV) in the systemic host Nicotiana benthamiana. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from the leaves of 5-week-old plants inoculated with TMV (1 mg/mL) or mock inoculated with sterile water.

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Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection

Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome This microarray can be useful to study gene activity of Arabidopsis thaliana associated with response to virus infection. For ecotypes ST-0, Wt-1, Ler-0, Di-2 there are five biological replicates and for ecotype Oy-0 there are three. As control we used four technical replicates of each ecotype, but five for Ler-0. Rows and columns are numbered as scanned by a GenePix Scanner (barcode on the bottom, DNA on the front surface).

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Project description:In this study, we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem associated translatomes in Prunus domestica L. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2), as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from plum leaves taken at 2, 4 and 6 weeks post vernalization.

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Project description:Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology. Over 100,000 TMV-Cg-specific small RNA reads, mostly of 21- (78.4%) and 22-nucleotide (12.9%) in size and originating predominately (79.9%) from the genomic sense RNA strand, were captured at an early infection stage, yielding the first high-resolution small RNA map for a plant virus. The TMV-Cg genome harbored multiple, highly reproducible small RNA-generating hot spots that corresponded to regions with no apparent local hairpin-forming capacity. Significantly, both the rdr1 and rdr6 mutants exhibited globally reduced levels of viral small RNA production as well as reduced strand bias in viral small RNA population, revealing an important role for these host RDRs in viral siRNA biogenesis. In addition, an informatics analysis showed that a large set of host genes could be potentially targeted by TMV-Cg-derived siRNAs for posttranscriptional silencing, raising the interesting possibility for a hidden layer of widespread virus-host interactions that may contribute to viral pathogenicity and host specificity. Profiling of TMV-Cg derived small RNAs in systemically infected tissues of wild type (Col-0) Arabidopsis as well as the rdr1and rdr6 mutants, at 3 days post-infection.

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Phloem tissue specific genome-wide open chromatin state in Arabidopsis thaliana.

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