Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Species

Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the family (DNA transposons) contributed to the speciation of Stål, 1859. This hypothesis motivated us to study two additional species of the complex: da Rosa et al., 2012 and Souza et al., 2016, together with a new, de novo annotation of the repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of . We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily as well as members of the LINE order (Class I). In addition to , we also identified a recent burst of transposition of the Mariner family in and , suggesting that this phenomenon may not be exclusive to . Rather, we hypothesize that whilst the expansion of elements may have contributed to the diversification of the - species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs.