LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.

Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes, shaping genome structure and evolution; however, their chromosomal distribution and lineage-specific dynamics remain incompletely understood. Here, we analyzed the abundance, spatial organization, and evolutionary history of intact LTR-RTs across 208 plant species using highquality chromosome-level genomes and the MegaLTR tool. Our analyses reveal extensive interspecific variability in LTR-RTs composition and chromosomal organization. Across families, LTR-RTs distributions are significantly non-random, with chromosome identity strongly influencing accumulation patterns. Although both Copia and Ty3-retrotransposons superfamilies exhibit significant inter-chromosomal heterogeneity, these superfamilies differ in the dimension of their non-randomness: Copia elements show more frequent heterogeneity between chromosomes, while Ty3-retrotransposons display stronger within-chromosome spatial structuring, consistent with preferential accumulation in recombination-suppressed heterochromatic regions. Distinct lineage patterns were observed, including highly structured Ty3-retrotransposons distributions in Poaceae. Insertion time analyses across 16 major clades revealed significant differences between genic and intergenic regions, with most clades showing younger insertions within genes. This pattern supports the role of purifying selection in removing older deleterious insertions from functional sequences. Together, these findings demonstrate that although regulatory mechanisms of LTR-RTs are broadly conserved, their chromosomal landscapes are shaped by superfamily-specific behavior, lineage history, and selective constraints, highlighting the central role of transposable elements in plant genome evolution.