The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution

Abstract

Genes in pieces and spliceosomal introns are a landmark of eukaryotes, with intron invasion usually assumed to have happened early on in evolution. Here, we analyze the intron landscape of Micromonas, a unicellular green alga in the Mamiellophyceae lineage, demonstratingthe coexistence of several classesof introns andtheoccurrence of recentmassive intron invasion. This study focuseson twostrains,CCMP1545andRCC299,andtheir related individuals fromoceansamplings, showingthat they notonly harbordifferent classes of introns depending on their location in the genome, as for other Mamiellophyceae, but also uniquely carry several classes of repeat introns. These introns, dubbed introner elements (IEs), are found at novel positions in genes and have conserved sequences, contrary to canonical introns. This IE invasion has a huge impact on the genome, doubling the number of introns in the CCMP1545 strain. We hypothesize that each IE class originated from a single ancestral IE that has been colonizing the genome after strain divergence by inserting copies of itself into genes by intron transposition, likely involving reverse splicing. Along with similar cases recently observed in other organisms, our observations in Micromonas strains shed anewlight on the evolution of introns, suggesting that intron gain is more widespread than previously thought.