ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development

Alba, Rob; Fei, Zhangjun; Payton, Paxton; Liu, Yang; Moore, Sally Falk; Debbie, Paul; Cohn, Jonathan; D’Ascenzo, Mark; Gordon, J.; Rose, Jocelyn K. C.; Martin, Gregory B.; Tanksley, Steven D.; Bouzayen, Mondher; Jahn, Molly M.; Giovannoni, Jim

doi:10.1111/j.1365-313x.2004.02178.x

Cited by 222 publications

(173 citation statements)

References 122 publications

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“…html) contain 13,400 printed elements corresponding to approximately 8,700 unigenes (Alba et al, 2004).…”

Section: Hybridization and Data Acquisitionmentioning

confidence: 99%

“…To investigate gene expression changes during fruit development in mesocarp and locular tissue, we monitored the transcriptome of these tissues during the expansion phase in tomato (Fig. 6A) using TOM1 cDNA microarray slides (Van der Hoeven et al, 2002;Alba et al, 2004). MA-ANOVA analysis followed by elimination of low-quality data on the basis of background threshold and flags (see "Materials and Methods") allowed the selection of 1,139 spots with a significant variation of expression (P , 0.01 and false discovery rate [FDR] , 0.05).…”

Section: Mesocarp and Locular Tissue Follow Parallel Metabolite Trajementioning

confidence: 99%

“…Coexpression analyses allowed the identification of genes regulating tissue and cell development (Persson et al, 2005;Gifford et al, 2008), environmental responses , and plant metabolism Gutiérrez et al, 2008) and were further validated by reverse genetics strategies. With the current availability of large-scale gene expression and metabolite profiling techniques in many plants, including tomato (Alba et al, 2004(Alba et al, , 2005Lemaire-Chamley et al, 2005;Moco et al, 2006;Mounet et al, 2007;Saito et al, 2007;Mintz-Oron et al, 2008;Schauer et al, 2008), large gene expression and metabolite data sets can be combined through correlation and clustering analyses (Urbanczyk-Wochniak et al, 2003) and further represented as a network of relationships between genes and metabolites Saito et al, 2007;Hoefgen and Nikiforova, 2008). These approaches have been successfully applied to the discovery of regulatory and biosynthetic genes involved in the control of metabolite production, such as the glucosinolate metabolism (Hirai et al, 2004.…”

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confidence: 99%

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Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

et al. 2009

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Variations in early fruit development and composition may have major impacts on the taste and the overall quality of ripe tomato (Solanum lycopersicum) fruit. To get insights into the networks involved in these coordinated processes and to identify key regulatory genes, we explored the transcriptional and metabolic changes in expanding tomato fruit tissues using multivariate analysis and gene-metabolite correlation networks. To this end, we demonstrated and took advantage of the existence of clear structural and compositional differences between expanding mesocarp and locular tissue during fruit development (12-35 d postanthesis). Transcriptome and metabolome analyses were carried out with tomato microarrays and analytical methods including proton nuclear magnetic resonance and liquid chromatography-mass spectrometry, respectively. Pairwise comparisons of metabolite contents and gene expression profiles detected up to 37 direct gene-metabolite correlations involving regulatory genes (e.g. the correlations between glutamine, bZIP, and MYB transcription factors). Correlation network analyses revealed the existence of major hub genes correlated with 10 or more regulatory transcripts and embedded in a large regulatory network. This approach proved to be a valuable strategy for identifying specific subsets of genes implicated in key processes of fruit development and metabolism, which are therefore potential targets for genetic improvement of tomato fruit quality.

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“…html) contain 13,400 printed elements corresponding to approximately 8,700 unigenes (Alba et al, 2004).…”

Section: Hybridization and Data Acquisitionmentioning

confidence: 99%

Section: Mesocarp and Locular Tissue Follow Parallel Metabolite Trajementioning

confidence: 99%

mentioning

confidence: 99%

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Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

et al. 2009

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“…The misrepresentation of PHD-finger homeobox genes may be due to their atypical sequence features. These genes usually have extremely long transcripts that might impair reverse transcription and/or subsequent cDNA cloning (Alba et al, 2004).…”

Section: Phylogenetics Analysismentioning

confidence: 99%

Identification and characterization of homeobox genes in Eucalyptus

et al. 2005

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Homeobox genes encode transcriptional factors, usually involved in molecular control of plant developmental patterns. They can be divided into several classes according to conserved sequences within the homeobox region and the presence of specific additional sequences. Based on these conserved sequences, we developed a search procedure to identify possible homeobox genes in the Eucalyptus Genome Sequencing Project Consortium (FORESTs) database. We were able to identify 50 Eucalyptus sequences (EST-contigs) containing the homeodomain sequence. Phylogenetic analysis was applied to this ESTs-contigs and 44 of them were found to have similarities with one of three well-known homeobox classes: Bell, Knox and HD-Zip, and their sub-classes. However, no EST-contig grouped with the fourth important homeobox class, the PHD-finger homeobox. On the other hand, two sequences have showed pronounced similarity to the Arabidopsis thaliana Wuschel gene, considered an "atypical" homeobox gene. Hierarchical clustering analysis of the expression pattern of these putative Eucalyptus homeobox genes revealed the presence of ten distinct expression groups. Combining phylogenetic analysis and expression patterns for some of the Eucalyptus genes revealed interesting aspects about some of the potential homeobox genes, which might lead to a better understanding of the Eucalyptus biology and to biotechnological applications.

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“…1), an approach referred to as eNorthern, in silico or digital expression profiling (Alba et al 2004). In addition to simply scoring EST frequencies, mathematical approaches were developed to associate a test statistic with a predicted differential gene expression (Stekel et al 2000).…”

Section: Global Approach I: High-throughput Est-sequencing Provides Amentioning

confidence: 99%

Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula

Hohnjec

Henckel

Bekel

et al. 2006

Functional Plant Biol.

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Abstract. The arbuscular mycorrhizal (AM) association between terrestrial plants and soil fungi of the phylum Glomeromycota is the most widespread beneficial plant-microbe interaction on earth. In the course of the symbiosis, fungal hyphae colonise plant roots and supply limiting nutrients, in particular phosphorus, in exchange for carbon compounds. Owing to the obligate biotrophy of mycorrhizal fungi and the lack of genetic systems to study them, targeted molecular studies on AM symbioses proved to be difficult. With the emergence of plant genomics and the selection of suitable models, an application of untargeted expression profiling experiments became possible. In the model legume Medicago truncatula, high-throughput expressed sequence tag (EST)-sequencing in conjunction with in silico and experimental transcriptome profiling provided transcriptional snapshots that together defined the global genetic program activated during AM. Owing to an asynchronous development of the symbiosis, several hundred genes found to be activated during the symbiosis cannot be easily correlated with symbiotic structures, but the expression of selected genes has been extended to the cellular level to correlate gene expression with specific stages of AM development. These approaches identified marker genes for the AM symbiosis and provided the first insights into the molecular basis of gene expression regulation during AM.

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ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development

Cited by 222 publications

References 122 publications

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

Identification and characterization of homeobox genes in Eucalyptus

Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula

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