Journal Article

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

Peng, Xiao-Yi, Gong, Zhi-Chao, Mao, Shi-Qing

2026

Overview

Background 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. Results In this study, IS 200 /IS 605 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 IS H3 family. Notably, genes flanking these IS H3 insertions were frequently associated with environment-related metabolic functions, suggesting that IS H3 proliferation may contribute to adaptation to high-temperature environments. Sequence analysis further revealed overlaps between IS and ELT elements, including IS 630 –Tc1/ mariner and IS 3 /IS 481 –LTR/ Gypsy associations, while phylogenetic analysis of DDE transposases indicated extensive cross-domain gene exchange. Conclusions 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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Annotations / Archaea / Archaea - classification / Archaea - genetics / Archaeal genome / Bacteria / Biomedical and Life Sciences / Datasets / DDE / DDE transposases / DNA Transposable Elements - genetics / Eukaryotes / Evolution, Molecular / Evolutionary genetics / Genes / Genome, Archaeal / Genomes / Genomics - methods / High temperature / High temperature environments / Insertion / Insertion Sequences / Life Sciences / Microarrays / Microbial Genetics and Genomics / Nitrous oxide / Phylogenetics / Phylogeny / Plant Genetics and Genomics / Prokaryotes / Proteins / Proteomics / Sequence analysis / Transposable elements / Transposons