Ontology highlight
ABSTRACT:
PROVIDER: PRJNA936910 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23560421_1.fastq.gz | Fastqsanger.gz | |||
| SRR23560421_2.fastq.gz | Fastqsanger.gz | |||
| SRR23560422_1.fastq.gz | Fastqsanger.gz | |||
| SRR23560422_2.fastq.gz | Fastqsanger.gz | |||
| SRR23560423_1.fastq.gz | Fastqsanger.gz |
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Project description:In this study we analyzed the effects of CRY2 over-expression on chloroplast genome transcription of tomato, by developing and using a tiling array. This array containing about 90,000 overlapping probes (5-nt resolution) is a versatile tool for global functional studies of tomato cp genome. We profiled transcription in leaves of wild-type (WT) and CRY2-overexpressing (CRY2-OX) plants grown in a diurnal cycle, to generate a comprehensive map of plastid transcription and to monitor potential specific modulations of chloroplast transcriptome induced by the overexpression of CRY2.
2016-06-24 | E-MTAB-1757 | biostudies-arrayexpress
Project description:Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome.
2011-08-02 | GSE23626 | GEO
Project description:Purpose: Many studies have demonstrated that ZFPs have important functions in many biological processes, including plant growth and development, stress response, and phytohormone response. RanBP2-type zinc finger transcription factors have been characterized in animals and humans. However, their functions remain largely unknown in plants. Therefore, the functions of RanBP ZFPs in plants need further study to shed new insights into the importance of these transcription factors in developmental processes. Methods: The transcriptomes of between overexpression of SlRBZ transgenic and wild-type tomato by RNA-seq analysis were evaluated using the Illumina HiSeq⢠2000 sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by Tophat and DEGseq software. qRTâPCR validation was performed using SYBR Green assays. Results: In this study, we identified a RanBP2-type zinc finger protein gene (SlRBZ) in tomato. SlRBZ was constitutively expressed in roots, stems, leaves, flowers and fruits. Overexpression of SlRBZ resulted in etiolated and dwarf phenotypes in tomato. Determination of physiological index showed that chlorophyll, carotenoid, and GAs contents were evidently decreased in transgenic plants. Furthermore, the qRT-PCR and RNA-Seq analyses demonstrated that the transcription of the genes involved in these biosynthesis pathways obviously decreased in SlRBZ-OE plants. In addition, ultrastructural observation by transmission electron microscopy indicated that plastids could not develop into mature chloroplasts with normal chloroplast membrane and thylakoid membrane system in SlRBZ-OE plants. Conclusions: The results suggest that overexpression of SlRBZ may impair the biosynthesis of chlorophyll, carotenoid, and gibberellin through blocking chloroplast development, resulting in etiolation and dwarfism in tomato. The transcriptomes of between overexpression of SlRBZ transgenic and wild-type tomato by RNA-seq analysis were evaluated, in duplicate, using the Illumina sequencing platform.
2016-01-29 | E-GEOD-77340 | biostudies-arrayexpress
Project description:Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome. Total RNA was isolated from psaA and psbA tobacco mutant plants along with the wild type plants. Biotin labeled cRNA was hybridized on tomato GeneChip Genome Array following the Affymetrix protocols. Two independent biological replicates were maintained.
2011-08-01 | E-GEOD-23626 | biostudies-arrayexpress
Project description:To explore the molecular mechanism via which the galactinol synthase 2 (slgols2) affects Chl accumulation and chloroplast development, the RNA-seq experiment was conducted using slgols2 mutant and WT tomato fruits.
2024-03-12 | GSE261229 | GEO
Project description:Purpose: Many studies have demonstrated that ZFPs have important functions in many biological processes, including plant growth and development, stress response, and phytohormone response. RanBP2-type zinc finger transcription factors have been characterized in animals and humans. However, their functions remain largely unknown in plants. Therefore, the functions of RanBP ZFPs in plants need further study to shed new insights into the importance of these transcription factors in developmental processes. Methods: The transcriptomes of between overexpression of SlRBZ transgenic and wild-type tomato by RNA-seq analysis were evaluated using the Illumina HiSeq™ 2000 sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by Tophat and DEGseq software. qRT–PCR validation was performed using SYBR Green assays. Results: In this study, we identified a RanBP2-type zinc finger protein gene (SlRBZ) in tomato. SlRBZ was constitutively expressed in roots, stems, leaves, flowers and fruits. Overexpression of SlRBZ resulted in etiolated and dwarf phenotypes in tomato. Determination of physiological index showed that chlorophyll, carotenoid, and GAs contents were evidently decreased in transgenic plants. Furthermore, the qRT-PCR and RNA-Seq analyses demonstrated that the transcription of the genes involved in these biosynthesis pathways obviously decreased in SlRBZ-OE plants. In addition, ultrastructural observation by transmission electron microscopy indicated that plastids could not develop into mature chloroplasts with normal chloroplast membrane and thylakoid membrane system in SlRBZ-OE plants. Conclusions: The results suggest that overexpression of SlRBZ may impair the biosynthesis of chlorophyll, carotenoid, and gibberellin through blocking chloroplast development, resulting in etiolation and dwarfism in tomato.
2016-01-29 | GSE77340 | GEO
Project description:The whitefly, Bemisia tabaci MEAM1 is a devastating vector capable of transmitting hundreds of plant viruses, including Tomato yellow leaf curl virus (TYLCV), to important food and fiber crops. Here we performed genome-wide profiling of micro RNAs (miRNAs) and piwi-interacting RNAs (piRNAs) in whiteflies after feeding on TYLCV-infected tomato or uninfected tomato for 24, 48 and 72 h. Overall, 160 miRNAs were discovered, 68 of which were conserved and 92 were B. tabaci-specific miRNAs. Majority of the genes that were predicted to be targeted by miRNAs had gene ontologies related to metabolic processes. We identified two miRNAs that were differentially expressed in whiteflies when fed on TYLCV-infected tomato compared to whiteflies that fed on uninfected tomato. The identified piRNAs were expressed as clusters throughout the whitefly genome. A total of 53 piRNA clusters were expressed across all time points and treatments, while 5 piRNA clusters were exclusively expressed in whiteflies that fed on TYLCV-infected tomato, and 24 clusters were exclusively expressed in whiteflies that fed on uninfected tomato. Approximately 62% of all identified piRNAs were derived from non-coding sequences that included intergenic regions, introns, and UTRs with unknown functions. The remaining 38% of piRNAs were derived from coding sequences (CDS) and repeat elements. Transposable elements targeted by piRNA clusters included both class I retrotransposons such as Gypsy, Copia, and LINEs and class II DNA transposons such as MITE, hAT, and TcMar. Lastly, six protein coding genes were targeted in whiteflies that fed on TYLCV-infected tomato. Information on how TYLCV influences miRNA and piRNA expression in whiteflies provides a greater understanding of regulatory pathways involved in mediating whitefly-virus interactions, and will facilitate the identification of novel targets for RNAi control.
2019-02-28 | GSE111343 | GEO
Project description:Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato’s world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,254 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 550 and 105 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 88 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.
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