Next-Generation Sequencing of the Tomato Transcriptome: a Resource for SNP Discovery, High Throughput Genotyping and Translational Research

Bioinformatic and computational comparison of sequences within and across species has empowered basic and applied research.  The identification of Conserved Ortholog Set (COS) genes, the ability to predict intron sequences based on reference genomes, and databases organized around metabolic pathways have further facilitated comparative analysis.  Next generation sequencing is now providing much more extensive sequence data and genomic resources that extend horizontally to encompass variation within and between species.  To assess the genetic diversity within tomato germplasm, we constructed normalized cDNA libraries from six inbred tomato varieties using root, leaf, flowers, fruit and callus tissue. Using Illumina GAII “next generation” sequencing technology, we generated >2.5 Gb of total sequence for each tomato cultivar, respectively.  The 60 bp reads, single and paired end, were assembled using Velvet to generate 32.5 Mb of transcriptome sequence from tomato.  These new sequences give us tools for further analysis of the Solanaceae genome landscape, including identification of gene duplications between species, a compendium of tomato Single Nucleotide Polymorphisms (SNPs), a description of haplotype blocks across domesticated lineages, and the proportion of the genome under purifying/diversifying selection.  These data provide resources to facilitate applied objectives while also providing a description of the effect of human selection on genomes of Horticultural Crops.