Full-length cDNA nanopore sequencing of ripe fruit samples from Heinz 1706 and TS-666

Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,904 TE insertions polymorphisms (TIPs) produced by the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and they are disproportionately located within or adjacent to genes involved in environmental response. In addition, many genic TIPs have strong transcriptional effects and we uncovered ~160 TIPs associated with extreme variations in fruit color or secondary metabolites. Moreover, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest that TE mobilization played a unique and important role in tomato diversification, with important implications for future breeding.