The Tomato 150 Genome Project Uncovers Structural Variation in the Tomato Clade

84 genotypes, including 10 old varieties, 42 landraces and 30 wild relatives of tomato have been sequenced using Illumina HiSeq as representatives of the four major phylogenetic groups in the tomato clade (www.tomatogenome.net). Furthermore, three wild species, Solanum arcanum, Solanum habrochaites and Solanum pennellii have been sequencing using both 454 and Illumina HiSeq, with the goal to construct new reference genomes. Using these sequencing data, patterns of structural variation have been identified.

We studied allelic variation in the twelve phylogenetic groups of the tomato clade and identified patterns of structural variation such as duplications and deletions and patterns of introgression have been identified. Ratios of synonymous and non-synonymous SNPs have been determined. In addition, a collection of tag SNPs, useful for further genetic studies in tomato, has been identified. The identified structural variation has been uploaded into a JBrowse Genome Browser and will be publicly available via www.tomatogenome.net. Larger structural variations have been studied by comparing synteny between the four available reference genomes for the tomato clade. The data provide a valuable resource to facilitate tomato genetics and breeding.