Résumé
Transposable elements (TEs) are mobile genetic elements capable of moving within a genome via two main mechanisms: retrotransposition with a copy-and-paste mechanism and DNA transposition with a cut-and-paste mechanism. In yeast, the majority of TEs are Long Terminal Repeat (LTR) retrotransposons. However, a novel type of DNA transposon was discovered in the Saccharomycotina yeast Diutina catenulata, which we named Dici for Diutina catenulate Invader. This new element of ~4 kb in size exhibits short Terminal Inverted Repeats (TIRs) and is structurally related to the Tc1/mariner superfamily. It displays a unique organization with three coding sequences (CDSs), including a CDS encoding a transposase that is oriented in the opposite direction to the other two. Based on this structure, the element represents a new family within the Tc1/mariner group. Two types of Dici DNA transposons have been identified in D. catenulata. Dici type 1 (Dici1) is abundant only in the reference strain CBS 565, with 96 complete copies, together with a Miniature Inverted-repeat Transposable Element (MITE) and 9 degenerate copies. Dici type 2 (Dici2) is present in numerous copies in all of the 56 D. catenulata strains we studied. Population genomic analysis of these 56 D. catenulata strains revealed highly divergent clades with predominantly clonal propagation, indicating the early stages of speciation. These clades showed significant genetic diversity and numerous chromosomal rearrangements. Transposable elements appear to play a crucial role in these genomic rearrangements. A striking example is a 300 kb segmental duplication flanked by two Dici1 elements. Interestingly, each Dici type showed very low internal sequence diversity, suggesting a recent transposition burst. In addition, the insertion point of the Dici elements varies inside clades, suggesting that the elements are still active.