Horizontal transmission of functionally diverse transposons is a major source of new introns

Specialized transposable elements (TEs), introners, are one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. We analyze 8716 genomes, revealing 1093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species, and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that intron gain is an inevitable consequence of TE activity in eukaryotic lineages, thereby resolving a key mystery of genome structure evolution.