Decoding horizontal transposon transfer across plants through a comprehensive HTT atlas

Horizontal transposon transfer (HTT) plays an important role in genome evolution; however, its prevalence, evolutionary patterns, and potential mechanisms in plants remain poorly understood due to limited taxonomic sampling and challenges in distinguishing HTT from vertical inheritance.

This study aimed to systematically identify HTT events across major plant lineages, investigate factors potentially associated with HTT, and assess the possible evolutionary significance of HTT in plant genomes.

A total of 558 high-quality plant genomes representing 352 species spanning algae to angiosperms were analyzed. A conservative phylogeny-informed framework integrating transposable element (TE) annotation, orthology inference, sequence similarity analysis, and lineage distribution filtering was developed to identify putative HTT events. Co-transfer relationships, host gene enrichment, transport-related pathways, and exosome-associated sequences were further analyzed to investigate candidate factors associated with HTT.

In total, 1,548 putative HTT events involving 684 TE families were identified across diverse plant lineages, indicating that both RNA- and DNA-mediated transposons contribute extensively to HTT in plants. Co-transfer analyses revealed widespread associations among TE superfamilies, whereas functional enrichment analyses highlighted chromatin-related and transport-related host genes frequently associated with HTT regions. HTT-related TE sequences were also detected in publicly available plant exosomal sequencing datasets, and several hotspot TE families showed homology to viral-associated sequences, suggesting potential involvement of vesicle-mediated transport and viral interactions in HTT processes. In addition, genes associated with cold acclimation and stress responses were enriched near several HTT regions, suggesting that HTT may contribute to environmental adaptation in some plant lineages.

This study provides a comprehensive atlas of HTT across plants and establishes a scalable framework for HTT detection in large-scale comparative genomics analyses. These findings generate candidate hypotheses regarding the mechanisms and evolutionary significance of HTT and provide a resource for future functional and experimental investigations.