MiBASE: A database of a miniature tomato cultivar Micro-Tom

Abstract

The miniature cultivar Micro-Tom has attracted much attention as a model of tomato (Solanum lycopersicum) because it has small size (10-20 cm in height), a short life cycle (70-90 days), and grows well in ordinary laboratory spaces. Recently, expressed sequence tag data and full-length cDNA sequences have been accumulated for Micro-Tom. To provide genomic information resource for Micro-Tom, we constructed the MiBASE database, which can be access via the Internet at http://www.kazusa.or.jp/jsol/microtom/. In addition to sequence information, this database contains information on simple sequence repeats, single nucleotide polymorphisms between other tomato inbred lines, nonredundant sequence sets, gene ontology terms, metabolic pathway names, and gene expression data.

Tissue- and Cell-Type Specific Transcriptome Profiling of Expanding Tomato Fruit Provides Insights into Metabolic and Regulatory Specialization and Cuticle Formation

“…Research resources for tomato include linkage maps, extensive mapping and breeding germplasm collections (Gur et al, 2004;Bombarely et al, 2011), and a substantial molecular and genomic toolbox (Yano et al, 2006;Bombarely et al, 2011;Fei et al, 2011), including the release and updates of a high-quality genome sequence (http://solgenomics.net). This infrastructure has promoted major advances in the study of fruit molecular biology, physiology, and biochemistry and more recently has laid the foundation for large-scale profiling of tomato fruit transcriptomes (Alba et al, 2004(Alba et al, , 2005Wang et al, 2009;Osorio et al, 2011), proteomes (Faurobert et al, 2007;Yeats et al, 2010;Catalá et al, 2011), and metabolomes (Bino et al, 2005;Nashilevitz et al, 2010).…”

Genomic Databases for Tomato

“…Information on tomato unigene sequences is provided in the TIGR Tomato Gene Index database (Lee et al 2005), the Solanaceae Genome Project Network (SGN) (Mueller et al 2005b) and the database MiBASE (Yano et al 2006a , predicted peptide sequences and InterProScan annotations (including domains, GO terms and gene families). DNA markers are searchable with the graphical chromosome maps described above.…”

“…MiBASE provides information on 26,363 tomato unigenes (version January, 2005) assembled from 150,581 publicly available ESTs in dbEST (Boguski et al 1993) and 35,824 Micro-Tom ESTs from fruit and leaves (Yamamoto et al 2005;Yano et al 2006a). In MiBASE, BLAST annotations based on the Arabidopsis translated protein sequence database in TAIR and the TIGR Gene Indices of rice, soybean (Glycine max), maize (Zea mays) and tomato have been released, as well as annotations from the NCBI nr database.…”

Web Databases for Omics Data in Tomato

“…Information on tomato unigene sequences is provided by the DFCI Tomato Gene Index database (Lee et al, 2005), the SGN (Mueller et al, 2005a), and the MiBASE (Yano et al, 2006b (Rhee et al, 2003), predicted peptide sequences, and InterProScan annotations (including domains, GO terms, and gene families). MiBASE provides information on 26,363 tomato unigenes (version KTU1, January, 2005) assembled from 150,581…”

“…ESTs in dbEST (Boguski et al, 1993) (Yamamoto et al, 2005;Yano et al, 2006b). MiBASE contains BLAST annotations based on the Arabidopsis translated protein sequence database in TAIR and the TIGR Gene Indices, as well as annotations from the NCBI nr database.…”