Retrolyc1 subfamilies defined by different U3 LTR regulatory regions in the Lycopersicon genus

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Abstract
Retrolyc1, a Ty1/copia-like element, was originally isolated from the Lycopersicon peruvianum genome and shown to be present also in other Lycopersicon species. It shares extensive similarities with Tnt1, except in its U3 regulatory region. In order to evaluate Retrolyc1 diversity, we analyzed partial sequences including both coding domains and the U3 regulatory region in four different species of the Lycopersicon genus. Two Retrolyc1 subfamilies defined by different U3 regions were identified. Retrolyc1A is most abundant in L. peruvianum and L. hirsutum, while Retrolyc1B is distributed in all four species studied here. The Retrolyc1A U3 region contains tandemly repeated elements of 53 bp. Transient expression analysis suggests that Retrolyc1A is a transcriptionally active family, and that the repeated motifs found in its U3 region are important transcriptional regulatory elements.

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