Comparative Analysis of Active LTR Retrotransposons in Sunflower (Helianthus annuus L.): From Extrachromosomal Circular DNA Detection to Protein Structure Prediction

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (<i>Helianthus annuus</i>), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the <i>Tekay</i> clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that <i>Athila</i> RTEs and <i>Tekay</i> group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the <i>Tekay</i> subgroup exhibited remarkable conservation among over 500 <i>Tekay</i> members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower <i>Tekay</i> aORF protein showed significant homology with <i>Tekay</i> proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins.