Proteins and ncRNAs across 352 species illuminate genome evolution

Transposable elements (TEs), nature’s genetic engineers’, are pivotal drivers of genome evolution, yet their precise mechanisms in shaping plant functional innovation remain elusive. This study presents a comprehensive analysis of TEs across 558 high-quality plant genomes, encompassing 352 species from 221 genera across five phyla, ranging from algae to angiosperms. We identified over 460 million TEs and 67 million transposase domains, systematically assessing their impact on host genomes through gene domestication, noncoding RNA generation, and gene duplication. Our analysis revealed 1,258,230 genes domesticated from TEs, 1,165,059 ncRNAs originating from TEs, and 10,488,967 TE-induced gene duplications. These genes affect more than 2,805 function families, likely planning crucial roles at key stages of plant evolution.