A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis.

Intronic sequences represent a large fraction of most eukaryotic genomes, and they are known to play a critical role in genome evolution. Based on the conserved location of introns, conserved sequence within introns, and direct experimental evidence, it is becoming increasingly clear that introns perform important functions such as modulating gene expression. Here, we demonstrate that the positions of 69% (862/1246) of human introns in 343 orthologous genes are conserved in the starlet sea anemone Nematostella vectensis, a phylogenetically basal animal (phylum Cnidaria; class Anthozoa). This degree of intron concordance greatly exceeds that between humans and three more closely related animals: fruitfly (14%), mosquito (13%) and nematode worm (19%). Surprisingly, the fruitfly and mosquito, two members of the order Diptera, share only 43% of intron locations, fewer than the percentage of cumulative introns shared between human and sea anemone (47%), despite sharing a much more recent common ancestor. Our analysis indicates (1) that early animal genomes were intron-rich, (2) that a large fraction of introns present within the human genome likely originated early in evolution, before the cnidarian-bilaterian split, at least 600 million years ago, and (3) that there has been a high degree of intron loss during the evolution of the protostome lineage leading to the fruitfly, mosquito, and nematode. These data also reinforce the conclusion that there are functional constraints on the placement of introns in eukaryotic genes.