Comparing gene expression between wild type and trichomeless mutants
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE9597 | GEO | 2008/04/30
SECONDARY ACCESSION(S): PRJNA103441
REPOSITORIES: GEO
Similar Datasets
Project description:Trichomes are found on the leaf surface of many plant species. They can be classified into either glandular or non-glandular types. Glandular trichomes are usually multicelluar structures and have long been known to participate in defense against pathogens through the production of specialized chemical products. Non-glandular trichomes, such as those in Arabidopsis thaliana, have been hypothesized to have roles in physical defense against insects, UV protection, detoxification, and heat dispersal. However, it has been difficult to separate a physical role from other possible functions for non-glandular trichomes. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes. Experiment Overall Design: We compared the gene expression between the wild type and three trichomeless mutants: gl1, ttg1 and gl3egl1 to see which genes' transcripts are enriched in trichomes.
2008-06-16 | E-GEOD-9597 | biostudies-arrayexpress
Project description:Trichomes are the hair-like structures that are widely present on the surface of aerial organs and function in plant defense against biotic and abiotic stresses. Previous studies focus on the single cell trichomes in Arabidopsis and cotton, or multicellular glandular trichomes in tomato, but the developmental process and molecular mechanisms controlling multicellular non-glandular trichome development are largely neglected. Here, we extensively characterized the fruit trichome (spine) development in wild type cucumber and in a tiny branched hair (tbh) mutant that contains a spontaneous mutation and has hairless foliage and smooth fruit surface. Our data indicated that cucumber trichome was multicellular and non-glandular, with no branches or endoreduplication. Further, the major feature of cucumber trichome development was spine base expansion. Transcriptome profiling through Digital Gene Expression indicated that meristem-related genes and transcription factors were implicated in the fruit spine development, and polarity regulators were upregulated during spine base expansion. qRT-PCR verified the reliability of our RNA-SEQ data, and in situ hybridization confirmed the enriched expression of meristem regulators CUP-SHAPED COTYLEDON3 (CUC3) and STM (SHOOT MERISTEMLESS) , as well as the abaxial identity gene KANADI (KAN) in cucumber fruit spine. Together, our results suggest a distinct regulatory pathway involving meristem genes and polarity regulators in multicellular trichome development in cucumber.
2014-07-01 | GSE49607 | GEO
Project description:Trichomes are the hair-like structures that are widely present on the surface of aerial organs and function in plant defense against biotic and abiotic stresses. Previous studies focus on the single cell trichomes in Arabidopsis and cotton, or multicellular glandular trichomes in tomato, but the developmental process and molecular mechanisms controlling multicellular non-glandular trichome development are largely neglected. Here, we extensively characterized the fruit trichome (spine) development in wild type cucumber and in a tiny branched hair (tbh) mutant that contains a spontaneous mutation and has hairless foliage and smooth fruit surface. Our data indicated that cucumber trichome was multicellular and non-glandular, with no branches or endoreduplication. Further, the major feature of cucumber trichome development was spine base expansion. Transcriptome profiling through Digital Gene Expression indicated that meristem-related genes and transcription factors were implicated in the fruit spine development, and polarity regulators were upregulated during spine base expansion. qRT-PCR verified the reliability of our RNA-SEQ data, and in situ hybridization confirmed the enriched expression of meristem regulators CUP-SHAPED COTYLEDON3 (CUC3) and STM (SHOOT MERISTEMLESS) , as well as the abaxial identity gene KANADI (KAN) in cucumber fruit spine. Together, our results suggest a distinct regulatory pathway involving meristem genes and polarity regulators in multicellular trichome development in cucumber. Using Digital Gene Expression technology to compare the genome-wide gene expression profiles in the fruit spines of wild type cucumber and the tbh mutant, as well as the fruit spines on fruits of 0.5cm and 1.6cm long, repectively. Two biological repelicates were generated for each tissue.
2014-07-01 | E-GEOD-49607 | biostudies-arrayexpress
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
Project description:The development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. Genetic studies have revealed that a bHLH transcription factor, GL3, activates downstream genes required for trichome initiation by interacting with a R2R3-MYB protein, GL1. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes.
2009-03-02 | GSE12522 | GEO
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 development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. Genetic studies have revealed that a bHLH transcription factor, GL3, activates downstream genes required for trichome initiation by interacting with a R2R3-MYB protein, GL1. We have taken advantage of several mutants in the trichome developmental pathway and gene expression analyses to identify a set of genes expressed predominantly in Arabidopsis trichomes. Experiment Overall Design: We compared the gene expression between the wild type and trichome mutant, gl3 egl3 using green tissue (not include root).
2009-03-07 | E-GEOD-12522 | biostudies-arrayexpress
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. Here, the transcript raw and RMA-normalized data is hosted.
2017-05-31 | E-MTAB-4482 | biostudies-arrayexpress
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:The MYB gene family encodes transcription factors with a diverse range of functions in Arabidopsis. This study demonstrated that MYB5, which is expressed in trichomes and seeds, plays a central role in trichome and seed development. A microarray analysis of myb5 seeds identified other members of the MYB5 regulatory network.
2009-03-02 | GSE14229 | GEO