ArticlePlant molecular biology2006
Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf.
Article in Plant molecular biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 1 of them a synthesis that pooled it.
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47 citing papers in PubMed, 1 synthesis or guideline pooled it, 120 citations in OpenAlex.
- Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa.BMC genomics · 2009Pooled it
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- Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing withInternational journal of molecular sciences · 2019Article
- Integrative comparative analyses of metabolite and transcript profiles uncovers complex regulatory network in tomato (Solanum lycopersicum L.) fruit undergoing chilling injury.Scientific reports · 2019Article
- Regulation of the Central Carbon Metabolism in Apple Fruit Exposed to Postharvest Low-Oxygen Stress.Frontiers in plant science · 2019Review
- The Agrobacterium F-Box Protein Effector VirF Destabilizes the Arabidopsis GLABROUS1 Enhancer/Binding Protein-Like Transcription Factor VFP4, a Transcriptional Activator of Defense Response Genes.Molecular plant-microbe interactions : MPMI · 2018Article
- OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies.Frontiers in plant science · 2017Article
- Genome-Wide Identification and Analysis of Genes, Conserved betweenFrontiers in plant science · 2017Article
- Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- The Glycerol-3-Phosphate Acyltransferase GPAT6 from Tomato Plays a Central Role in Fruit Cutin Biosynthesis.Plant physiology · 2016Article
- Nitric Oxide Mediated Transcriptome Profiling Reveals Activation of Multiple Regulatory Pathways in Arabidopsis thaliana.Frontiers in plant science · 2016Article
- Transcriptome Profiling of Huanglongbing (HLB) Tolerant and Susceptible Citrus Plants Reveals the Role of Basal Resistance in HLB Tolerance.Frontiers in plant science · 2016Article
- Fungal endophyte infection of ryegrass reprograms host metabolism and alters development.The New phytologist · 2015Article
- Integrated metabolomics and transcriptomics reveal enhanced specialized metabolism in Medicago truncatula root border cells.Plant physiology · 2015Article
- Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.PloS one · 2015Article
- Metabolic control of redox and redox control of metabolism in plants.Antioxidants & redox signaling · 2014Review
- On the role of plant mitochondrial metabolism and its impact on photosynthesis in both optimal and sub-optimal growth conditions.Photosynthesis research · 2014Review
- Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.Rice (New York, N.Y.) · 2013Article
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Authors and funding
13 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tomato microarray TOM1 offers the possibility to monitor the levels of several thousand transcripts in parallel. The microelements represented on this tomato microarray have been putatively assigned to unigenes, and organised in functional classes using the MapMan ontology (Thimm et al., 2004. Plant J. 37: 914-939). This ontology was initially developed for use with the Arabidopsis ATH1 array, has a low level of redundancy, and can be combined with the MapMan software to provide a biologically structured overview of changes of transcripts, metabolites and enzyme activities. Use of this application is illustrated using three case studies with published or novel TOM1 array data sets for Solanaceous species. Comparison of previously reported data on transcript levels in potato leaves in the middle of the day and the middle of the night identified coordinated changes in the levels of transcripts of genes involved in various metabolic pathways and cellular events. Comparison with diurnal changes of gene expression in Arabidopsis revealed common features, illustrating how MapMan can be used to compare responses in different organisms. Comparison of transcript levels in new experiments performed on the leaves of the cultivated tomato S. lycopersicum and the wild relative S. pennellii revealed a general decrease of levels of transcripts of genes involved in terpene and, phenylpropanoid metabolism as well as chorismate biosynthesis in the crop compared to the wild relative. This matches the recently reported decrease of the levels of secondary metabolites in the latter. In the third case study, new expression array data for two genotypes deficient in TCA cycle enzymes is analysed to show that these genotypes have elevated levels of transcripts associated with photosynthesis. This in part explains the previously documented enhanced rates of photosynthesis in these genotypes. Since the Solanaceous MapMan is intended to be a community resource it will be regularly updated on improvements in tomato gene annotation and transcript profiling resources.
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