Where the Minor Things Are: A Pan-Eukaryotic Survey Suggests Neutral Processes May Dominate Minor Spliceosomal Intron Evolution

Abstract

Spliceosomal introns are gene segments removed (“spliced”) from RNA transcripts by large ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second spliceosome (the minor/ U12-type) is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying and cataloging minor introns in > 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers of minor introns in some fungi and green algae, repeated massive loss, as well as several general biases in the positional and genic distributions of minor introns. We estimate that ancestral minor intron densities were comparable to those of the most minor intron-rich species, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, we find highly similar patterns of minor and major intron evolution, in contrast to the predictions of both functionalist and deleterious models. Second, we find that observed functional biases among minor intron-containing genes are largely explained by these genes’ greater ages. Third, we find no association of intron splicing with cell proliferation in a minor intronrich fungus, suggesting that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing’s persistence. These data constitute the most comprehensive view to date of modern minor introns, their evolutionary history, and the forces shaping minor splicing, and provide a foundation for future studies of these remarkable genomic elements.