Insights into plant LINE evolution: Essential domains persist amidst widespread structural degeneration

Plant long interspersed nuclear elements (LINEs) are structurally diverse, experience periodic pulses of degeneration, and occur in lower copy numbers than LTR retrotransposons. Consequently, their macroevolutionary dynamics remain poorly understood. Here, we curated a high-stringency reverse transcriptase (RT) database to annotate structurally complete LINEs across 54 plant genomes spanning from Marchantiopsida to Magnoliopsida. The highly selective filtering yielded a refined dataset dominated by L1 and RTE families, whereas I, R2, and Jockey superfamilies were rare and highly degenerate. Full-length elements retained at least essential ORF2 domains (EEP and RT) alongside a 3′ poly(A) tail. However, those of longer length exhibited structural variability, carrying 5′ ORF1 regions, non-essential ORF2 domains (Zf-RVT and RNH), and, in some cases, 3′ (GTT)n motifs before the poly(A) tail. L1 elements were larger and showed greater EEP-RT domain heterogeneity than RTE. Nonetheless, RT-based phylogeny robustly separated these two groups. An alignment-free k-mer-based pipeline (k = 9) validated our manual annotations and successfully resolved degraded domains and interstitial gaps missed by conventional BLAST alignments. Furthermore, genomic abundance showed only a moderate positive correlation with genome size, underscoring lineage-specific TE dynamics. Overall, our findings demonstrate that plant LINE evolution is driven by widespread structural degeneration, where the selective persistence of core catalytic domains (RT and EEP) sustains element survival amidst extensive domain loss across land plants.