Evolution of Tat Retrotransposons Reveals Mosaic Phylogenetic Patterns Among Land Plants

Transposable elements (TEs) are rarely used as phylogenetic markers because of their high copy number, frequent recombination, and potential for horizontal transfer. However, their long-term coexistence with host genomes suggests that some TE lineages may preserve information about the evolutionary history of their genomic environment. Here, we investigate whether Tat LTR retrotransposons of the Ty3/Gypsy superfamily retain a phylogenetic signal informative for deep plant evolution. We reconstructed the phylogeny of Tat reverse transcriptase domains among representative lineages of land plants, including bryophytes, lycophytes, ferns, gymnosperms, and basal angiosperms. The analysis revealed stable clusters characterized by both structural specificity, determined by the position of the additional ribonuclease H domain, and taxonomic specificity. In many cases, the Tat subclusters reproduced established host relationships at the genus and family levels, particularly within conifers, indicating a predominantly vertical mode of inheritance. The distribution of Tat lineages also preserved signals relevant to unresolved questions of plant phylogeny. Among seed plants, different Tat lineages reflected aspects of existing alternative hypotheses, including the association of gnetophytes both with conifers II and angiosperms. Interestingly, the strong separation between two major conifer groups, pines and cypress with yews, was observed. Among non-seed plants, the topology of Tat lineages highlighted the unique position of lycophytes by the preservation of multiple ancient transposon lineages associated with early diversification after aRNH domain acquisition. It also suggested that the origins of mosses and hornworts involved different patterns of lineage elimination from a common ancestor that carried all structures found in lycophytes. We propose a conceptual framework in which TE clusters are interpreted as collections of partially independent evolutionary lineages rather than as a single species tree. Under this view, Tat retrotransposons provide an additional layer of phylogenetic information that complements conventional molecular markers and reflects the mosaic nature of plant genome evolution. The present work, therefore, represents the first implementation of this approach rather than its final methodological form.