Comprehensive profiling of insertion sequences and eukaryotic-like transposons across archaeal genomes

Transposable elements (TEs) are major drivers of genome plasticity, yet their diversity, dynamics, and evolutionary history remain poorly understood in archaea, which share a more recent common ancestry with eukaryotes than with bacteria. To address this issue, we systematically characterized insertion sequences (ISs), the predominant class of prokaryotic TEs, together with eukaryotic-like transposons (ELTs) across 17,237 archaeal genomes from 21 archaeal phyla. In this study, IS200/IS605 was the most widespread and abundant IS family across archaeal genomes. Although most archaeal phyla exhibited low IS and ELT content, we identified lineage-specific expansions and high IS family diversity within extremophilic groups, particularly the Thermoproteota and Halobacteriota. Analysis of complete genomes identified an IS-rich lineage within Sulfolobaceae, where genome size positively correlated with IS abundance. In the genus Saccharolobus, the increase in IS content was driven predominantly by the expansion of the ISH3 family. Notably, genes flanking these ISH3 insertions were frequently associated with environment-related metabolic functions, suggesting that ISH3 proliferation may contribute to adaptation to high-temperature environments. Sequence analysis further revealed overlaps between IS and ELT elements, including IS630–Tc1/mariner and IS3/IS481–LTR/Gypsy associations, while phylogenetic analysis of DDE transposases indicated extensive cross-domain gene exchange. Collectively, this large-scale survey illuminates the diversity, distribution, and evolutionary dynamics of transposable elements in archaea, providing new insights into their evolutionary connections with prokaryotes and eukaryotes.