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

<div><p>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 <i>S. pimpinellifolium</i> 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 <a href="http://59.163.192.91/tomato2/" target="_blank">http://59.163.192.91/tomato2/</a>.</p></div

Heat map showing genes preferentially/specifically expressed in four tissue samples.

<p>The number of genes and tissue specificity is noted at the right side. The color scale (0–50) represents RPKM values.</p

Schematic illustration showing the flow of the organization of the data in tomato genome database.

<p>Schematic illustration showing the flow of the organization of the data in tomato genome database.</p

Differential expression profiles of genes present in two collinear blocks located on chromosome 1 and 2.

<p>The color scale (0–20) represents RPKM values. IDs of the genes in the collinear blocks in chromosome 1 and 2 are mentioned in the left and right sides, respectively.</p

Chromosomal distribution and duplication of <i>14-3-3</i> genes.

<p><b>a</b> Maize. <b>b</b> Sorghum. <b>c</b> Foxtail millet. Vertical bars represent chromosomes and the values at left indicate the position of genes in megabase. Genes are marked in the right and Zm, Sb and Si denotes <i>Zea mays</i>, <i>Sorghum bicolor</i> and <i>Setaria italica</i>, respectively. Lines denote segmental duplication, whereas tandemly duplicated genes are highlighted in boxes.</p

Si14-3-3 and mutant SiRSZ21A (<i>m2</i> and <i>m3</i>) co-expressed in onion epidermal cells.

<p>Localization of m2 in nucleus is evidenced. <b>A</b> whole cell, <b>B</b> magnified view of nucleus.</p

Tissue-specific expression profiles of <i>14-3-3</i> genes.

<p><b>a</b> Sorghum. <b>b</b> Maize. <b>c</b> Foxtail millet. Illumina RNA-seq data of different tissues of these crops were re-analyzed and heat map was generated. Bar at the right represents log₂ transformed values, thereby values -3.0, 0.0 and 3.0 represent low, intermediate and high expression, respectively.</p

Yeast two-hybrid assay between Si14-3-3_f and SiRSZ21A.

<p>Y2H gold was co-transformed with both the constructs. Interaction was confirmed by culturing the co-transformants on selective media. Empty-BD constructs were used against the SiRSZ21A as controls. Autoactivation was also checked for SiRSZ21A.</p

Phylogenetic tree and gene organization of 14-3-3 proteins.

<p>The unrooted phylogenetic tree was constructed with maize 14-3-3 proteins from sorghum (Sb14-3-3), maize (Zm14-3-3), foxtail millet (Si14-3-3), <i>Arabidopsis</i> (GRF) and rice (GF). The intron-exon positions of respective members are shown in the right.</p

Screenshots of a map view and a gene description page showing various features of tomato genome database.

<p>Screenshots of a map view and a gene description page showing various features of tomato genome database.</p