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Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

ABSTRACT: Gene expression analysis of chrysanthemum infected with three different viruses including Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X have been performed using the chrysanthemum 135K microarray.

ORGANISM(S): Chrysanthemum

PROVIDER: GSE55985 | GEO | 2015/01/01

SECONDARY ACCESSION(S): PRJNA241631

REPOSITORIES: GEO

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Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

Project description:Gene expression analysis of chrysanthemum infected with three different viruses including Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X have been performed using the chrysanthemum 135K microarray. Mock and each virus infected chrysanthemum plants were subjected for microarray analysis.

2015-01-01 | E-GEOD-55985 | biostudies-arrayexpress

Chrysanthemum

Project description:Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

| PRJNA241631 | ENA

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

Cucumber green mottle mosaic virus

Project description:Cucumber green mottle mosaic virus Raw sequence reads

| PRJNA454023 | ENA

Cucumber mosaic virus resistance: Comparative proteomics of contrasting Cucumis sativus cultivars after long-term infection

Project description:Plant viruses are a major threat for a wide range of host species, causing substantial losses in agriculture. Particularly, Cucumber mosaic virus (CMV) evokes severe symptoms, thus dramatically limiting yield. Activation of plant immunity is associated with changes in the gene expression and consequently, cellular proteome to ensure virus resistance. Proteomics proved to be an extremely valuable tool for discovering multiple targets for the rational design of plant protection strategies. Herein, we studied two cultivars of cucumber (Cucumis sativus) resistant ´Heliana´ and susceptible ´Vanda´. Plant cotyledons were mechanically inoculated with CMV isolate PK1, and systemic leaves were harvested at 33 days post-inoculation. Upon protein extraction and filter-aided sample preparations, peptides were profiled by ultrahigh-performance liquid chromatography and comprehensively quantified by ion mobility enhanced mass spectrometry. From 1,516 reproducibly quantified proteins using label-free approach, 133 were differentially abundant among genotypes or treatments by strict statistic and effect size criteria. Pigments and hydrogen peroxide measurements corroborated proteomic findings. Advanced bioinformatics revealed a modular network of affected host proteins. Direct comparison of both genotypes in the uninfected state highlighted more abundant photosynthetic and development-related proteins in resistant cucumber cultivar. Long-term CMV infection showed worse preservation of energy processes and less robust translation in susceptible cultivar versus resistant genotype. Contrary, susceptible cultivar had numerous more abundant stress and defense-related proteins. We proposed promising targets for functional validation in transgenic lines a step toward durable virus resistance in cucurbits and other crops.

2020-01-09 | PXD015088 | Pride

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

Transcriptional profiling of wilt-resistant and wilt-susceptible chickpea cultivars after Fusarium oxysporum f.sp. ciceri (Foc) inoculation

Project description:Purpose: Molecular analysis of chickpea-Foc interaction; Methods: Four LongSAGE libraries of wilt-resistant and wilt-susceptible chickpea cultivars prepared after Foc inoculation and sequenced using Ion Torrent PGM. Results: Transcriptome analyses revealed expression of several plant defense and pathogen virulence genes with their peculier expression patterns in wilt-resistant and wilt-susceptible chickpea cultivars. Conclusion: The study identified several candidate Foc resistant genes, which can be used for crop improvement after their functional validation.

2017-08-21 | GSE86377 | GEO

Proteomes and Histone Crotonylation Analysis Reveals the Importance of Crotonylation Low Temperature in Chrysanthemum

Project description:Chrysanthemum is a garden plant with good economic benefit and high ornamental value. Chrysanthemum in the key period of flowering in autumn and winter, vulnerable to cold damage, affecting the normal growth of the chrysanthemum plant and even death. little is known regarding the study of histone crotonylation in plant cold response. In this study, we first obtained reference chrysanthemum transcriptome data via RNA sequencing. Next, we quantitatively investigated the chrysanthemum proteome, crotonylation, and the association between them in chrysanthemum following low temperature. In total, 365669 unigenes, 6693 proteins and 2017 crotonylation sites were quantified under low temperature stress. There were 24631 up-regulated and 22648 down-regulated unigenes (absolute log2-fold change > 1 and P value<0.05), 393 up-regulated and 500 down-regulated proteins using a 1.2-fold threshold (P<0.05). The lysine crotonylation mainly influenced in photosynthesis, ribosome, antioxidant enzyme and ROS system. In the process of low temperature, 61 lysine crotonylation sites in 89 proteins were up-regulated and 87 lysine crotonylation sites in 72 proteins are down-regulated (1.2-fold threshold, P<0.05).

2021-01-04 | PXD010297 | Pride

Tomato spotted wilt virus benefits a non-vector arthropod Tetranychus urticae by modulating different plant responses in tomato

Project description:Five-week old tomato plants were subjected to four treatments: 1) mock-inoculated, 2) virus-infected, 3) spider mite infestation, and 4) virus + spider mite infestation. Plant tissue was harvested from each treatment after 7-days, frozen in liquid nitrogen and stored in -80 degree Celsius until use.

2013-05-15 | E-MEXP-3888 | biostudies-arrayexpress

Organ specific expression in cucumber

Project description:We compared organ specific chloroplast gene expression in cucumber between fully developed leaves (12th counting from the bottom of plant) and growing tips, female flowers, young leaves, young fruits (3-5 cm long). We have also characterized chloroplast gene transcription in cucumber etiolated seedlings in comparison to mature cucumber leaves.

2011-06-30 | E-MEXP-3227 | biostudies-arrayexpress

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