Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

Fei, Zhangjun; Joung, Je-Gun; Tang, Xuemei; Zheng, Yi; Huang, Mingyun; Lee, Je Min; McQuinn, Ryan P.; Tieman, Denise M.; Alba, Rob; Klee, Harry J.; Giovannoni, James J.

doi:10.1093/nar/gkq991

Cited by 110 publications

(85 citation statements)

References 30 publications

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“…In Figure 6B, the flg22 highly induced WRKY TRANSCRIPTION FACTOR53 (WRKY53) expression but not PR-1b in tomato. This result was consistent with the public RNA-seq data in the Tomato Functional Genomics Database (Fei et al, 2011), which are based on the experiment "transcriptome sequencing of tomato leaves treated with different bacteria and PAMPs" (Rosli et al, 2013). The RNA-seq data showed that WRKY53 could be induced but PR-1b, Adi3, and ERF5, but could not be significantly induced using 30 min or 6 h treatment of flg22 on the tomato.…”

Section: Bioactivity Of Cape1supporting

confidence: 86%

Quantitative Peptidomics Study Reveals That a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato

et al. 2014

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Many important cell-to-cell communication events in multicellular organisms are mediated by peptides, but only a few peptides have been identified in plants. In an attempt to address the difficulties in identifying plant signaling peptides, we developed a novel peptidomics approach and used this approach to discover defense signaling peptides in plants. In addition to the canonical peptide systemin, several novel peptides were confidently identified in tomato (Solanum lycopersicum) and quantified to be induced by both wounding and methyl jasmonate (MeJA). A wounding or wounding plus MeJA-induced peptide derived from the pathogenesis-related protein 1 (PR-1) family was found to induce significant antipathogen and minor antiherbivore responses in tomato. This study highlights a role for PR-1 in immune signaling and suggests the potential application of plant endogenous peptides in efforts to defeat biological threats in crop production. As PR-1 is highly conserved across many organisms and the putative peptide from At-PR1 was also found to be bioactive in Arabidopsis thaliana, our results suggest that this peptide may be useful for enhancing resistance to stress in other plant species.

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Section: Bioactivity Of Cape1supporting

confidence: 86%

Quantitative Peptidomics Study Reveals That a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato

et al. 2014

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“…Based on the evolutionary conservation of coexpression in the Solanaceae family, Miozzi et al (2010) developed the data-mining tool, ORTom, which predicts functional relationships among tomato genes. The Tomato Functional Genomics Database (TFGD) offers a Web-based retrieval tool for coexpressed genes (Fei et al, 2011). There are several differences between our approach and these previous studies.…”

Section: Discussionmentioning

confidence: 99%

“…We collected 307 GeneChips from publicly available databases including GEO, ArrayExpress (Parkinson et al, 2011), and TFGD (Fei et al, 2011) and included 20 of our own hybridizations (GEO accession no. GSE35020), resulting in a total of 327 arrays.…”

Section: Data Collection and Preprocessingmentioning

confidence: 99%

“…Gene ontology of tomato genes was based on information from TFGD (Fei et al, 2011). To assign the Sol Genomics Network (SGN) unigene (Mueller et al, 2005;Bombarely et al, 2011), similarity searches between the Affymetrix probe set identifier and the SGN unigene were performed using BLASTN (Altschul et al, 1990) with a threshold E value of 1e-10.…”

Section: Gene Annotationmentioning

confidence: 99%

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Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

Fukushima

Nishizawa²,

Hayakumo³

et al. 2012

Plant Physiology

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Gene-to-gene coexpression analysis provides fundamental information and is a promising approach for predicting unknown gene functions in plants. We investigated various associations in the gene expression of tomato (Solanum lycopersicum) to predict unknown gene functions in an unbiased manner. We obtained more than 300 microarrays from publicly available databases and our own hybridizations, and here, we present tomato coexpression networks and coexpression modules. The topological characteristics of the networks were highly heterogenous. We extracted 465 total coexpression modules from the data set by graph clustering, which allows users to divide a graph effectively into a set of clusters. Of these, 88% were assigned systematically by Gene Ontology terms. Our approaches revealed functional modules in the tomato transcriptome data; the predominant functions of coexpression modules were biologically relevant. We also investigated differential coexpression among data sets consisting of leaf, fruit, and root samples to gain further insights into the tomato transcriptome. We now demonstrate that (1) duplicated genes, as well as metabolic genes, exhibit a small but significant number of differential coexpressions, and (2) a reversal of gene coexpression occurred in two metabolic pathways involved in lycopene and flavonoid biosynthesis. Independent experimental verification of the findings for six selected genes was done using quantitative real-time polymerase chain reaction. Our findings suggest that differential coexpression may assist in the investigation of key regulatory steps in metabolic pathways. The approaches and results reported here will be useful to prioritize candidate genes for further functional genomics studies of tomato metabolism.

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“…The International Tomato Genome Sequencing Project started in 2004 by an international consortium including participants from Korea, China, United Kingdom, India, Netherlands, France, Japan, Spain, Italy and the United States and completed in 2012 (Tomato Genome Consortium 2012). Since then many databases and online tools have been developed to annotate full tomato genome (D'Agostino et al 2009;Grennan 2009;Fei et al 2011;Suresh et al 2014). Preliminary comparisons between the different Solanaceae members revealed synteny among various homologous genes (Wang et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Identification of key genes involved in root development of tomato using expressed sequence tag analysis

Kalidhasan

Joshi

Bhatt

et al. 2015

Physiol Mol Biol Plants

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Root system of plants are actually fascinating structures, not only critical for plant development, but also important for storage and conduction. Due to its agronomic importance, identification of genes involved in root development has been a subject of intense study. Tomato is the one of the most consumed vegetables in the world. Tomato has been used as model system for dicot plants because of its small genome, well-established transformation techniques and well-constructed physical map. The present study is targeted to identify of root specific genes expressed temporally and also gene(s) involved in lateral root and profuse root development. A total of 890 ESTs were identified from five EST libraries constructed using SSH approach which included temporal gene regulation (early and late) and genes involved in morphogenetic traits (lateral and profuse rooting). One hundred sixty-one unique ESTs identified from various libraries were categorized based on their putative functions and deposited in NCBI-dbEST database. In addition, 36 ESTs were selected for validation of their expression by RT-PCR. The present findings will help in shedding light to the unexplored developmental process of root growth in tomato and plant in general.

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Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

Cited by 110 publications

References 30 publications

Quantitative Peptidomics Study Reveals That a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato

Quantitative Peptidomics Study Reveals That a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

Identification of key genes involved in root development of tomato using expressed sequence tag analysis

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