The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high variability of its regulatory sequences

We studied the evolution of the tobacco Tnt1 retrotransposon by analyzingTnt1 partial sequences containing both coding domains and U3 regulatorysequences obtained from a number of Nicotiana species. We detected threedifferent subfamilies of Tnt1 elements, Tnt1A, Tnt1B, and Tnt1C, thatdiffer completely in their U3 regions but share conserved flanking codingand LTR regions. U3 divergence between the three subfamilies is found inthe region that contains the regulatory sequences that control theexpression of the well-characterized Tnt1-94 element. This suggests thatexpression of the three Tnt1 subfamilies might be differently regulated.The three Tnt1 subfamilies were present in the Nicotiana genome at the timeof species divergence, but have evolved independently since then in thedifferent genomes. Each Tnt1 subfamily seems to have conserved its abilityto transpose in a limited and different number of Nicotiana species. Ourresults illustrate the high variability of Tnt1 regulatory sequences. Wepropose that this high sequence variability could allow these elements toevolve regulatory mechanisms in order to optimize their coexistence withtheir host genome.