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ABSTRACT: TSWV genes differentially processed by RNAi in resistant tomato

PROVIDER: PRJNA606610 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11088875.fastq.gz	Fastqsanger.gz
	SRR11088876.fastq.gz	Fastqsanger.gz
	SRR11088877.fastq.gz	Fastqsanger.gz
	SRR11088878.fastq.gz	Fastqsanger.gz
	SRR11088879.fastq.gz	Fastqsanger.gz

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A TMT-based quantitative proteome analysis to elucidate the TSWV induced signaling cascade in susceptible and resistant cultivars of Solanum lycopersicum

Project description:Tomato spotted wilt virus (TSWV), transmitted by small insects known as thrips, is one of the major threats to tomato productivity across the globe. In addition to tomato, this virus infects more than 1000 other plants belonging to 85 families and is a cause of serious concern. Very little, however, is known about the molecular mechanim of TSWV induced signaling in plants. Here, we used a TMT-based quantitative proteome analysis to investigate the protein profiles of tomato leaves of two cultivars (cv 2621and 2689; susceptible and resistant respectively to TSWV infection) following TSWV inoculation. This approach resulted in the identification of 5112 proteins of which 1022 showed significant changes in response to TSWV. While the proteome of resistant cultivar majorly remain unaltered, proteome of susceptible cultivar showed distint differences following TSWV infection. TSWV modulated proteins in tomato included those with functions previously implicated in plant defence incuding secondary metabolism, ROS detoxification, MAP kinase signaling, Calcium signaling and jasmonate biosynthesis, among others. Taken together, these results provide new insights into the TSWV induced signaling in tomato leaves and may be useful in future to manage this deadly disease of plants.

2020-05-06 | PXD017250 | Pride

Microarray analysis of Lycopersicon esculentum plants subjected to tomato spotted wilt virus inoculation, western flower thrips infestation and a combination of virus and thrips

Project description:In the current study, we sought to elucidate the plant-mediated mechanisms underlying the interaction between TSWV and its insect vector, F. occidentalis in the plant host, tomato, Solanum lycopersicum L. We performed replicated greenhouse and laboratory experiments to confirm that TSWV altered vector performance and behavior in ways that improved virus transmission. To characterize plant molecular mechanisms, microarray analysis was done in tomato plants that were systemically-infected with TSWV, infested with thrips, or both TSWV and thrips using Affymetrix Tomato GeneChip®. The tomato microarray chip includes many defense- and stress-related genes and genes related to chloroplast function, cell wall modification, and protein synthesis which we hypothesized would be involved in TSWV-vector interaction.

2020-08-01 | E-MTAB-9294 | biostudies-arrayexpress

RNA-Seq analysis sheds light on the breakdown of Tomato spotted wilt virus resistance in pepper at high temperature

Project description:The Tsw gene conferring Tomato spotted wilt virus (TSWV) resistance in Capsicum chinense breaks down at high temperatures. Here, we performed RNA-Seq analysis under different temperature conditions to uncover the resistance breakdown mechanism using TSWV-resistant C. chinense ‘PI152225’ and susceptible ‘Habanero’. RNA-Seq analysis revealed only a few differentially expressed genes (DEGs) at 1 dpi but 2,096 and 551 DEGs between plants at 25°C and 30°C at 5 dpi. At 5 dpi, there were more upregulated than downregulated DEGs at both temperatures. Gene ontology analysis revealed 30 enriched biological process terms and nine molecular function terms that were enriched among upregulated DEGs at 25°C. We performed KEGG analysis with 805 upregulated DEGs at both temperatures to explore the mechanism underlying resistance breakdown at high temperature. The DEGs were mapped into 10 KEGG pathways. ACC oxidase genes in the ethylene biosynthesis pathway were differentially expressed upon pathogen challenge. Most DEGs from the biological process, molecular function, and cellular components categories involved in resistance responses were downregulated at 30°C. Finally, genes involved in abscisic acid-mediated stress signaling were differentially expressed at high temperature. These results shed light on host–virus interactions and temperature-dependent resistance mechanisms in pepper at the molecular level.

2019-06-01 | GSE124386 | GEO

Transcription profiling of tomato shoots and roots from plants systemically infected by TSWV reveals organ-specific transcriptional responses

Project description:Transcription profiling of roots and shoots of tomato plants as a result of systemic infection with the tospovirus Tomato Spotted Wilt Virus (TSWV).

2009-08-04 | E-MTAB-133 | biostudies-arrayexpress

Arbuscular mycorrhizal symbiosis limits foliar transcriptional responses to viral infection and favors long-term virus accumulation

Project description:Transcriptional changes triggered by the systemic infection of the tospovirus Tomato Spotted Wilt Virus (TSWV) in roots and shoots of tomato plants (Solanum lycopersicum) mycorrhized by Glomus mosseae

2011-10-31 | E-MTAB-620 | biostudies-arrayexpress

Transcriptome profiling of RNAi-trasgenic Solanum lycopersicum plants resistant to Tomato yellow leaf curl virus

Project description:RNA interference (RNAi) is a widely-used approach to generate virus-resistant transgenic crops. However, durability of RNAi-mediated resistance under extreme field conditions and side-effects of stable RNAi expression have not been thoroughly investigated. Here we performed field trials and molecular characterization of two RNAi-transgenic Solanum lycopersicum lines resistant to Tomato yellow leaf curl virus (TYLCV) disease, the major constraint for tomato cultivation in Cuba and worldwide. In order to determine potential impact of the hairpin RNA transgene expression on tomato genome expression and development, differences in the phenotypes and the transcriptome profiles between the transgenic and non-transgenic plants were examined. Transcriptome profiling revealed a common set of up- and down-regulated tomato genes, which correlated with slight developmental abnormalities in both transgenic lines.

2014-11-29 | GSE63708 | GEO

Identification of a host protein interacting with Tomato spotted wilt virus ribonucleoproteins from Nicotiana benthamiana and yeast.

Project description:Viruses are obligate intracellular pathogens that depend on host factors to complete their infection cycle. Very little is known of which plant factors are required for successful Tomato spotted wilt orthotospovirus (TSWV) infection. The viral ribonucleoprotein (RNP) fraction from TSWV infected Nicotiana benthamiana plants was purified and its protein composition was analysed by proteomics by mass spectrometry to identify host proteins that co-purify with viral RNPs. Related, we expressed a TSWV replicon system in a non-host system, Bakers’ yeast (Saccharomyces cerevisiae), and purified as well the RNP fraction from yeast. Comparative proteomics was used to find common enriched proteins observed in both yeast and plant RNP fractions.

2021-11-10 | PXD026246 | Pride

Role of SlPGR5 regulating proteomic remodeling in tomato leaves

Project description:Tandem mass tag labelling (TMT) based proteomics analysis was used to campare differentially expressed proteins (DEGs) between WT, SlPGR5-OE and SlPGR5-RNAi of tomato at normal and low night temperature condition

2022-06-15 | PXD034523 |

Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both plant and nematode during susceptible and resistance responses.

Project description:Purpose: To understand the molecular mechanisms involved in disease development during plant-nematode interactions. Methods: We have taken a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time points from susceptible plants (PR: Pusa Ruby) and two infection time points from resistant plants (M36: Transgenic MM line), grown under soil conditions. Results: Differentially expressed genes during susceptible (1827 tomato, 462 RKN) and resistance (25 tomato, 160 RKN) interactions were identified and a set of genes were validated by qRT-PCR. Conclusion: Our findings, for the first time, provide insights into the transcriptome dynamics of both tomato and RKN during susceptible and resistance interactions and reveal involvement of a complex network of biosynthetic pathways during disease development.

2017-08-21 | GSE88763 | GEO

Comparative transcriptome analysis between resistant and susceptible tomato lines uncovers the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum

Project description:Leaf mold disease caused by Cladosporium fulvum is a major disease in cultivated tomato plants and affects global tomato production. Some Cf genes, of which Cf-16 is an effective gene for resisting tomato leaf mold, are associated with leaf mold resistance; however, the molecular mechanism is largely unknown. We used comparative transcriptome analysis of C. fulvum-resistant (cv. Ontario7816, including the Cf-16 gene) and C. fulvum-susceptible (cv. Moneymaker) tomato lines to identify differentially expressed genes (DEGs) at 4 and 8 days postinfection with C. fulvum. Our results provide new insights into the resistance response mechanism of Cf genes to C. fulvum, especially the unique characteristics of Cf-16 in response to C. fulvum infection.

2020-01-06 | GSE133678 | GEO

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