Comparative analysis of transposable element landscapes in diploid and allotetraploid Trifolium reveals LTR-RT-driven subgenome divergence

Background Transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), are major drivers of plant genome evolution. In allopolyploids, TE landscapes can reflect both inherited differences between progenitor lineages and repeat evolution post-polyploidisation. These dynamics, however, are understudied in many non-model genera, including in the genus Trifolium (clover). With the recent availability of chromosome-scale Trifolium genome assemblies, this study characterises and compares TE landscapes across nine species of Trifolium (seven diploids, two allotetraploids). Results LTR-RTs dominated TE landscapes in Trifolium and accounted for most interspecific variation in repeat content. In diploids, genome size variation was strongly associated with TE content, while overall TE class composition remained broadly conserved. In both allotetraploids, T. dubium and T. repens , most TE families were shared between subgenomes, with subgenome repeat divergence driven primarily by differences in abundance among shared families rather than by subgenome-exclusive repertoires. Paired-LTR identity profiles indicated predominantly recent LTR-RT insertions across species, although species, superfamily, clade and subgenome-level differences were evident. Across the genus, solo:intact ratios indicated lineage-specific differences in recombination-mediated LTR-RT removal. Conclusions LTR-RTs are the main contributors to repeat variation in Trifolium . Subgenome repeat divergence in allotetraploids largely reflects differential abundance of shared TE families, with stronger subgenome differentiation in TE content and recent LTR-RT insertion activity in T. dubium than T. repens . Together, these results indicate lineage and family-specific differences in LTR-RT amplification, retention and removal across Trifolium .