Retrotransposons are suitable targets for developing molecular markers for population genetics studies. Transposable elements have not yet been isolated from ectomycorrhizal fungi of the genus Tuber. In this paper, we report on the isolation and characterization of Tmt1, an LTR-retrotransposon from Tuber melanosporum. The Tmt1 sequence shows relatedness to Ty3/gypsy retrotransposons from which it differentiates for the presence of a dUTPase extra-domain between protease and reverse transcriptase. Phylogenetic analyses suggest a horizontal transfer of the dUTPase gene (dut) from a fungal host genome. The presence of non-identical LTRs and degenerate ORFs substantiate an ancient integration of Tmt1 in T. melanosporum genome. Furthermore, transcripts analyses proved an inactive status of Tmt1, whereas Southern analysis showed that Tmt1 is a repetitive T. melanosporum species-specific element. Tmt1-based markers will help us to gain more insights into population biology in this fungal species
