Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research

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 create...

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Bibliographic Details
Published in:PloS one 2014-01, Vol.9 (1), p.e86387-e86387
Main Authors: Suresh, B Venkata, Roy, Riti, Sahu, Kamlesh, Misra, Gopal, Chattopadhyay, Debasis
Format: Article
Language:English
Subjects:
Agriculture
Biology
Browsing
Chromosomes
Data bases
Databases, Genetic
DNA, Plant - genetics
Domestication
Gene expression
Gene sequencing
Genes
Genetic diversity
Genetic Loci - genetics
Genome, Plant - genetics
Genomes
Genomics
Loci
Lycopersicon esculentum - genetics
MicroRNA
MicroRNAs - genetics
miRNA
Polymorphism, Single Nucleotide - genetics
Quantitative genetics
Quantitative trait loci
Relational data bases
Researchers
Ribonucleic acid
RNA
Simple sequence repeats
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Solanaceae
Solanum lycopersicum
Solanum pimpinellifolium
Studies
Tomatoes
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Description
Summary: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/.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0086387