De Novo Discovery and Comparison of Transposable Element Families in S. lycopersicum and S. pimpinellifolium
Solanum lycopersicum has fewer high-copy, full-length long terminal repeat (LTR) retrotransposons than Arabidopsis and sorghum, and the average insertion age is older (2.8 vs 0.8 mya). Tandem repeat families, telomeric repeats and other repeats are found in centromeres, telomeres and other heterochromatic regions. Transposable elements (TEs) are found in both heterochromatin and euchromatin. There is a lack of well characterized repeat libraries for Solanaceous species compared to grasses like rice and wheat.
The transposable elements in the domesticated tomato genome, S. lycopersicum heinz 1706, will be compared to S. pimpinellifolium (a close wild ancestor to domesticated tomato) as well as other more distant wild relatives and heirloom varieties and characterized by
•Within-family sequence similarity
•Indels in alignments
The identified transposable elements will be catalogued and available through the Sol Genomics network (SGN, http://solgenomics.net/), a clade oriented database and a repository for a large and growing number of solanaceae genomes. The collection of genomic data and computational resources of SGN provides the opportunity to study TEs across a phenotypically diverse and economically important plant family.