Different gene expression in the tomato trichome and leaf
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA483134 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7609950_1.fastq.gz | Fastqsanger.gz | |||
| SRR7609950_2.fastq.gz | Fastqsanger.gz | |||
| SRR7609951_1.fastq.gz | Fastqsanger.gz | |||
| SRR7609951_2.fastq.gz | Fastqsanger.gz | |||
| SRR7609952_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the transcriptome difference between glandular cells of type VI trichome and leaf cells of trichome shaved leaf.
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Project description:We report the effect of chalcone isomerase deficiency on gene expression of glandular cells of type VI trichome in tomato leaves.
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Project description:Tomato leaf stem and leaf blade type VI trichome head mRNA-seq
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Project description:Glandular trichomes (GT) are specialized cell factories that have the capacity to produce large amounts of metabolites which can amount to over 10% of the leaf dry weight. The specific expression of secondary metabolite pathways in glandular trichomes has facilitated their elucidation. However, little is known about the connection between central carbon and specialized metabolism in these cells. To address this question, we used the type VI glandular trichomes from a cultivated (Solanum lycopersicum LA4024) and a wild tomato accession (Solanum habrochaites LA1777) as a model. Our study is based on metabolomics, transcriptomics, proteomics and 13C-labeling datasets of trichome and leaves samples. This comparative analysis allowed us to identify specific features of trichomes in comparison to leaves. Tomato type VI trichomes are photosynthetic but acquire their carbon essentially from the leaves in the form of sucrose. Relatively high expression levels of photosystem genes and comparatively low expression of Calvin-cycle and photorespiration genes indicate that photosynthesis is used primarily to produce energy and reducing power to drive the high metabolic activity. High levels of polyunsaturated fatty acids, oxylipins, and of oxidized glutathione and high transcript and protein levels of associated enzymes further indicate a distinct capacity of GT to cope with oxidative stress. Enzymes which are involved in the supply of key precursors for the production of terpenoids both from the cytosol and in the chloroplasts are markedly increased. Finally, some enzymes that are typically associated with C4-photosynthesis are highly expressed in trichomes, suggesting that CO2 recycling processes may increase the efficiency of C usage in these cells. Based on this information we propose a model on how the glandular trichomes achieve high metabolic efficiency.
2017-07-04 | PXD003154 | Pride
Project description:Trichomes of Arabidopsis thaliana have been broadly used to study cell development, cell differentiation and cell wall biogenesis. In this context, the exposed position, extraordinary size and characteristic morphology of trichomes featured particularly the exploration of trichome mutant phenotypes. However, trichome-specific biochemical or -omics analyses require a proper separation of trichomes from residual plant tissue. Thus, different strategies were proposed in the past for trichome isolation, which mostly rely on harsh conditions. To improve trichome-leaf separation, we revised a previously proposed method for isolating A. thaliana trichomes by optimizing the mechanical and biochemical specifications for trichome release. Furthermore, we introduced a density gradient centrifugation step to remove residual plant debris. We found that prolonged, yet mild seedling agitation increases the overall trichome yield by about 62% compared to the original protocol. We noticed that subsequent density gradient centrifugation further visually enhances trichome purity, which could be advantageous for downstream analyses. Histochemical and biochemical investigation of trichome cell wall composition indicated that gentle agitation during trichome release largely preserves trichome integrity. We used enriched and purified trichomes for proteomic analysis and present a reference data set of trichome-resident and -enriched proteins.
2022-01-13 | PXD028808 | Pride
Project description:The occurrence of Tomato chlorosis virus (ToCV) disease seriously damages tomato growth and yield, and there is no effective way to control ToCV transmission. So far, no studies have reported exploring the interaction between ToCV and tomato at the single cellular level. In this study, single cell RNA sequence was performed on a total of 26720 individual cells from healthy and ToCV-infected tomato leaves. We through identifying cell types, the first tomato leaf cell atlas was successfully constructed. In situ hybridization experiments identified specific marker genes that can be used to identify tomato cell types. Moreover, we have characterized transcription factors that may play a key role in tomato response to ToCV infection, and described the trichome differentiation trajectory during ToCV infection through pseudotime analysis. In conclusion, we proved the feasibility of single-cell sequencing to study the response of plants to biotic stress, and put forward new insights into the interaction between ToCV and tomato from the cellular level. Our data will lay the foundation for following studies between ToCV and plants, and will also provide a valuable reference for future research on non-model plant single cells.
2024-05-01 | GSE201931 | GEO
Project description:Transcriptional profiling of leaf tissue processed for trichome isolation.
2009-02-04 | E-MEXP-2014 | biostudies-arrayexpress
Project description:Comparison of A. thaliana leaf pavement, trichome initial cells and mature trichomes
2007-11-14 | E-MEXP-1038 | biostudies-arrayexpress
Project description:Stem trichome mRNA-seq analysis of wild tomato relatives (Solanum section Lycopersicon)
| PRJEB44371 | ENA
Project description:Purpose: Plant trichomes are hair-like protuberances developing from epidermal cells of most terrestrial plants, serve as an excellent system for analyzing the molecular mechanisms underlying cell fate choices, cell cycle control, and cell morphogenesis. Regulation of trichomes in arabidopsis has been well characterized. However, the mechanisms of multicellular trichomes is unclear. To further identify the genes responsible for the SlCycB2-mediated phenotype change, we compared the gene expression profiles of SlCycB2-OE and RNAi plants by RNA-seq. Methods: The transcriptomes of between SlCycB2-OE and RNAi in tomato (Solanum lycopersicum) cultivar Ailsa Craig (AC) by RNA-seq analysis were evaluated using the Illumina HiSeq™ 2500 sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by Hisat2 and DEGseq software. qRT-PCR validation was performed using SYBR Green assays. Results: In this study, we determined that SlCycB2 encodes a nuclear localized protein, which is highly expressed in trichomes, stigmas, hypocotyls and stems, and induced by the light, suppressed under the dark. Transgene analysis showed that suppression of SlCycB2 could promote type III and type V trichomes formation. On the contrary, overexpression of SlCycB2 could result in nearly disappearance of all non-glandular trichomes (including type III and V), as well as the glandular ones of type I and type VI. Detection of secondary metabolites indicated that the production of monoterpene and sesquiterpene were significantly decreased in SlCycB2-OE plants, which thus caused the reduction of the defense against Prodenia litura. Transcriptome profile demonstrated that the differential expressed genes mainly participate in the biosynthesis of terpenes, cutin, suberine and wax. Furthermore, we identified several homologs of this gene in many plants, SlCycB3 in tomato, NtCycB2 in tobacco, AtCycB2 in Arabidopsis, which have similar regulatory functions in trichome formation. SlCycB2 overexpression also led to abnormal flower with the unclosed stamen, shortened style and aberrant pollen. Conclusions: The results demonstrate that SlCycB2 play a critical role in multicellular trichome formation, secondary metabolite biosynthesis, Prodenia litura defense and reproductive organ development in tomato. The similar roles of its homologs in multicellular trichome formation suggest that Solanaceous species may share common regulatory pathway.
2016-12-02 | GSE90747 | GEO