Genomic Databases for Tomato

Yano, Kentarô; Aoki, Koh; Shibata, Daisuke

doi:10.5511/plantbiotechnology.24.17

Cited by 17 publications

(11 citation statements)

References 51 publications

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“…Tomato is important not only as a vegetable crop from a commercial point of view but also as a model to study fruit physiology in basic research. A lot of information about tomato, including EST and full-length cDNA information can be obtained from databases such as the Sol Genomics Network ( http://www.solgenomics.net/ ) and TOMATOMICS ( http://www.bioinf.mind.meiji.ac.jp/tomatomics/ ) [23] . Also transcriptome data (at TOMATOMICS) and metabolome data of Solanaceae species (KaPPA-View4 SOL at http://www.kpv.kazusa.or.jp/kpv4-sol/ ) are available.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

et al. 2013

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The family of aquaporins, also called water channels or major intrinsic proteins, is characterized by six transmembrane domains that together facilitate the transport of water and a variety of low molecular weight solutes. They are found in all domains of life, but show their highest diversity in plants. Numerous studies identified aquaporins as important targets for improving plant performance under drought stress. The phylogeny of aquaporins is well established based on model species like Arabidopsis thaliana, which can be used as a template to investigate aquaporins in other species. In this study we comprehensively identified aquaporin encoding genes in tomato (Solanum lycopersicum), which is an important vegetable crop and also serves as a model for fleshy fruit development. We found 47 aquaporin genes in the tomato genome and analyzed their structural features. Based on a phylogenetic analysis of the deduced amino acid sequences the aquaporin genes were assigned to five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs) and their substrate specificity was assessed on the basis of key amino acid residues. As ESTs were available for 32 genes, expression of these genes was analyzed in 13 different tissues and developmental stages of tomato. We detected tissue-specific and development-specific expression of tomato aquaporin genes, which is a first step towards revealing the contribution of aquaporins to water and solute transport in leaves and during fruit development.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

et al. 2013

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“…Currently, most information from these resources has been released to databases in the public domain such as the National Center for Biotechnology Information (NCBI), the DNA Data Bank of Japan (DDBJ), the Solanaceae Genome Project Network (SGN), and the J. Craig Venter Institute (JCVI, formed through the merger of several organizations including The Institute for Genomic Research, TIGR). The current status of these tomato genomics databases has been reviewed by [ 23 ].…”

Section: Current State Of Tomato Genomicsmentioning

confidence: 99%

Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Matsukura

Aoki²,

Fukuda³

et al. 2008

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Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.

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“…Full-length cDNA libraries have been constructed from the fruit at different developmental stages and from pathogen-treated leaves of Micro-Tom. To date, information about 57,422 ESTs and 2,268 draft fulllength sequences have been made available in the KaFTom database Tsugane et al 2005;Yano et al 2007). …”

Section: Kaftommentioning

confidence: 99%

Omics databases in plant science: key to systems biology

Suwabe

Yano

2008

Plant Biotechnology

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This wealth of comprehensive online resources and web databases allows us to extract new essential biological information beyond what is gleaned from the dataset obtained from a single study. The large-scale data collected from web databases can be used to detect patterns such as consensus sequences of expressed sequence tags (ESTs) (e.g., Lazo et al. 2004;Lee et al. 2005;Lopez et al. 2004), global patterns of gene expression (Obayashi et al. 2007) and orthologous DNA and protein sequences among different genomes (Tatusov et al. 2003). To handle such large amounts of data effectively and efficiently, many new bioinformatics tools are under development. Here, we review the current state of web databases and bioinformatics tools available for plant research. The websites mentioned in this article are summarized in Table 1. Abstract Recently, high-throughput technologies for comprehensive genomic, transcriptomic and proteomic analyses have been developed. Large-scale 'omics data' obtained from such experimental methods have rapidly accumulated and been stored into web databases. In addition, the number of web databases for molecular biology has rapidly increased, since most new projects construct and maintain new web databases for their own large-scale omics data. This wealth of comprehensive online resources and web databases allow us to extract essential new biological information beyond a dataset obtained from an individual study. For effective and efficient handling of such large sets of data, various kinds of bioinformatics tools are being developed. Here, we review the current state of web databases and bioinformatics tools for plant biosciences and systems biology. Collections of databases, tools, and experimental materials

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Genomic Databases for Tomato

Cited by 17 publications

References 51 publications

Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Omics databases in plant science: key to systems biology

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