Tomato Genomic Resources Database: An Integrated Repository of Useful Tomato Genomic Information for Basic and Applied Research

B Venkata Suresh,Debasis Chattopadhyay,Riti Roy,Gopal Misra,Kamlesh Sahu,Tongming Yin

doi:10.1371/journal.pone.0086387

B Venkata Suresh, Debasis Chattopadhyay + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0086387

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Journal: PloS one	Publication Date: Jan 21, 2014
Citations: 85	License type: CC BY 4.0

Affiliation: National Institute of Plant Genome Research

Abstract

Tomato Genomic Resources Database (TGRD) allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether or separately along twelve chromosomes of tomato in a single window. The database is created using sequence of the cultivar Heinz 1706. High quality single nucleotide polymorphic (SNP) sites between the genes of Heinz 1706 and the wild tomato S. pimpinellifolium LA1589 are also included. Genes are classified into different families. 5′-upstream sequences (5′-US) of all the genes and their tissue-specific expression profiles are provided. Sequences of the microRNA loci and their putative target genes are catalogued. Genes and 5′-US show presence of SSRs and SNPs. SSRs located in the genomic, genic and 5′-US can be analysed separately for the presence of any particular motif. Primer sequences for all the SSRs and flanking sequences for all the genic SNPs have been provided. TGRD is a user-friendly web-accessible relational database and uses CMAP viewer for graphical scanning of all the features. Integration and graphical presentation of important genomic information will facilitate better and easier use of tomato genome. TGRD can be accessed as an open source repository at http://59.163.192.91/tomato2/.

Highlights

Tomato (Solanum lycopersicum) is model for a number of biological studies important to agriculture such as, fruit development and ripening, disease resistance and biochemical pathways of important nutrients [1,2,3]
Sequence Retrieval S. lycopersicum Heinz 1706 reference genome sequence, raw sequence reads of S. pimpinellifolium LA1589, latest annotation (ITAG 2.3), and gff files were downloaded from Sol genomics network database (SGN)
Tomato genome sequence has created a huge impact on Solanaceae research

Summary

Introduction

Tomato (Solanum lycopersicum) is model for a number of biological studies important to agriculture such as, fruit development and ripening, disease resistance and biochemical pathways of important nutrients [1,2,3]. Researchers from fourteen different countries together have published a reference genome sequence of an inbred tomato cultivar Heinz1706 and a draft sequence of wild tomato, Solanum pimpinellifolium [11] These sequence information have provided the basic and applied researchers an opportunity to scout for gene function, genetic diversity and evolution in tomato, and in other Solanaceae members, for studying basic biology and bio-diversity based breeding. There has been existence of a number of other tomato databases on specific aspects even before the release of tomato genome such as, SolEST database, MoTo DB, Tomato functional genomics database, miSolRNA, TOMATOMA, KaTomicsDB (http://www.kazusa.or.jp/tomato/) and several others [13,14,15,16,17,18] These databases serve extensively as resources for genomic and biochemical information and biological material for the Solanaceae research community. There is a need to amalgamate different genomic and trait information together graphically along all the chromosomes of tomato in a single window to enable the basic and applied researchers to integrate and utilize all the information in a better and easier way

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