Solanum tuberosum Nicotiana benthamiana Solanum lycopersicum
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PROVIDER: PRJNA766537 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome data of three hosts infected by Phytophthora infestation
| PRJNA766466 | ENA
Project description:Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.
| S-EPMC3842579 | biostudies-literature
Project description:BackgroundThe use of light emitting diodes (LEDs) brings several key advantages over existing illumination technologies for indoor plant cultivation. Among these are that LEDs have predicted lifetimes from 50-100.000 hours without significant drops in efficiency and energy consumption is much lower compared to traditional fluorescent tubes. Recent advances allow LEDs to be used with customized wavelengths for plant growth. However, most of these LED growth systems use mixtures of chips emitting in several narrow wavelengths and frequently they are not compatible with existing infrastructures. This study tested the growth of five different plant species under phosphor coated LED-chips fitted into a tube with a standard G13 base that provide continuous visible light illumination with enhanced blue and red light.ResultsThe LED system was characterized and compared with standard fluorescence tubes in the same cultivation room. Significant differences in heat generation between LEDs and fluorescent tubes were clearly demonstrated. Also, LED lights allowed for better control and stability of preset conditions. Physiological properties such as growth characteristics, biomass, and chlorophyll content were measured and the responses to pathogen assessed for five plant species (both the model plants Arabidopsis thaliana, Nicotiana bentamiana and crop species potato, oilseed rape and soybean) under the different illumination sources.ConclusionsWe showed that polychromatic LEDs provide light of sufficient quality and intensity for plant growth using less than 40% of the electricity required by the standard fluorescent lighting under test. The tested type of LED installation provides a simple upgrade pathway for existing infrastructure for indoor plant growth. Interestingly, individual plant species responded differently to the LED lights so it would be reasonable to test their utility to any particular application.
| S-EPMC4940826 | biostudies-literature
Project description:Rice stripe virus (RSV) causes the general chlorosis symptom and influences expression of numberous chloropalst-related genes at transcriotional level in Nicotiana benthamiana plants, but the mechanism are not well understood. Small RNAs (sRNAs), including virus-derived siRNA (vsiRNA) play roles in modulating genes expression post-transcriptionally. This present work presents multi-omics analysis of the transcriptome, sRNAome and degradome in RSV-infected N.benthamiana plants. Transcriptome-seq profiled 4127 N. benthamiana genes, with differentially expressed genes (DEGs) enriched in functional categories such as metabolic process, protein phosphorylation, regulation of transcription, carotenoid biosynthetic process. We identified 400863, 203874 and 244713 reads of vsiRNA from 3 sRNA libraries of RSV-infected N.benthamiana plants respectively. The degradome-seq report discovered a significant number of N.benthamiana genes that might be regulated by vsiRNAs post-transcriptionally. Based on integrated analysis of the three omics, we provide a substantial amount of novel information on the transcriptional and post-transcriptional networks in RSV-infected N.benthamiana, which will extends our horizon about the interactions between virus and their hosts.
2021-04-22 | GSE172507 | GEO
Project description:Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits. Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV). Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens. Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV. 3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum. Control plants were mock inoculated using sap from healthy plants. All plants were maintained in a growth chamber at 22C for 18 days. 8 plants were inoculated with each virus or mock inoculated. This experiment was repeated twice. 4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations. RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates. Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples. RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2. Total RNA was purified using Trizol according to TIGRs listed protocol. RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907). Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer. Keywords: Reference design
2007-09-01 | GSE8256 | GEO
Project description:Transcriptome profiling of Nicotiana benthamiana infected with CBSV and ACMV
| PRJNA378940 | ENA
Project description:Transcriptome profiling of Nicotiana benthamiana infected with CBSV and ACMV
| PRJNA378924 | ENA
Project description:Kac, a reversible PTM, plays essential roles in various biological processes, including those involving metabolic pathways, pathogen resistance and transcription, in both prokaryotes and eukaryotes. TMV, the major factor that causes poor quality of Solanaceae crops worldwide, directly alters many metabolic processes in tobacco. However, the extent and function of Kac during TMV infection have not been determined. Here, using LC−MS/MS in conjunction with highly sensitive immune-affinity purification, we comprehensively analyzed the changes in the proteome and acetylome of TMV-infected tobacco (Nicotiana benthamiana) seedlings. In total, 2082 lysine-acetylated sites on 1319 proteins differentially expressed in response to TMV infection were identified. Extensive bioinformatic studies disclosed changes in acetylation of proteins engaged in cellular metabolism and biological processes. The vital influence of Kac in fatty acid degradation and alpha-linolenic acid metabolism was also revealed in TMV-infected seedlings. This study first revealed Kac information in N. benthamiana under TMV infection and expands upon the existing landscape of acetylation in pathogen infection.
2022-10-15 | PXD035737 | Pride
Project description:This study aimed to investigate the physiological and molecular responses of Solanum lycopersicum (tomato) to Phytophthora cinnamomi infection. The initial defense response in tomato seeds included the production of reactive oxygen species (ROS) and callose deposition. Screening of commercial tomato varieties revealed varying levels of susceptibility, with the variety Marmande exhibiting heightened vulnerability. Three days post-inoculation, Marmande showed increased expression of genes associated with ROS generation, and biosynthesis pathways for phenylpropanoids and flavonoids. Additionally, 850 genes related to cell wall remodeling, including those involved in lignin biosynthesis and pectin methyl esterase inhibitors (PMEIs), were significantly upregulated. Seven days post-inoculation, a stronger transcriptional response was observed, with activation of ethylene (ET) and jasmonic acid (JA) signaling pathways, while salicylic acid (SA) showed minimal activity. Metabolomic analysis of infected roots revealed elevated levels of metabolites linked to lycopene, flavonoids, and phenylpropanoids. Furthermore, infected roots exhibited a significant reduction in pectin levels, which was corroborated by in vitro assays showing zoospore-mediated pectin degradation. These results suggest that degradation of root pectin is a key mechanism facilitating zoospore invasion in susceptible tomato hosts. This study provides new insights into the molecular mechanisms underlying host-pathogen interactions and identifies potential targets for managing Phytophthora cinnamomi-induced diseases in crops.
2025-04-29 | GSE295439 | GEO
Project description:Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits. Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV). Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens. Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV. 3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum. Control plants were mock inoculated using sap from healthy plants. All plants were maintained in a growth chamber at 22C for 18 days. 8 plants were inoculated with each virus or mock inoculated. This experiment was repeated twice. 4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations. RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates. Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples. RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2. Total RNA was purified using Trizol according to TIGRs listed protocol. RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907). Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer. Keywords: Reference design 23 hybs total
2007-09-01 | E-GEOD-8256 | biostudies-arrayexpress