Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Helianthus annuus L.) and Arabidopsis thaliana L.

Transposable elements (TEs) are ubiquitous components of plant genomes that profoundly influence plant diversity, adaptation, and genome structure. Transposition of TEs is primarily suppressed by distinct DNA methylation systems. However, the distribution of DNA methylation at the level of individual TEs in plants remains poorly understood. Here, we address this question by generating per-base cytosine methylation maps of individual long terminal repeat retrotransposons (LTR-RTEs) for the large sunflower (<i>Helianthus annuus</i> L.) and the small <i>Arabidopsis thaliana</i> genomes. <i>A. thaliana</i> was selected as the model species, for which genome-wide DNA methylation profiles have been extensively characterized in prior studies. Our analysis revealed significant heterogeneity in methylation patterns both between and within individual LTR-RTE lineages. We also found that the sunflower genes harboring intact or fragmented LTR-RTE insertions exhibit altered DNA methylation and expression profiles, with intact LTR-RTE insertions enriched in stress-response and regulatory pathways. Our interspecies comparison of DNA methylation patterns indicates that methylation patterns are intrinsic features of LTR-RTE lineages, conserved across diverse plant species but influenced by factors such as insertion age, element length, and proximity to genes. Furthermore, we identified epigenetically distinct clusters of <i>Tork</i> and <i>Athila</i> sunflower elements corresponding to separate phylogenetic clades, suggesting a link between epigenetic regulation and the genetic diversity of plant LTR-RTEs.