De novo creation of spliceosomal introns by different transposition mechanisms across diverse eukaryotes
Engineering
Corbett-Detig Lab
Introns are sequences interrupting genes that must be removed from mRNA before translation, and are a hallmark of eukaryotic genomes. They likely play important roles in genome evolution, but have poorly understood origins. Many species exhibit major intron loss events, which probably occur through RNA mediated homologous recombination of cDNA. In contrast, some species exhibit prolific intron gain. Micromonas pusilla, an aquatic picophytoplankton, probably exhibits the most notable recent case of intron gain. Intronic sequences known as introner elements (IEs) colonized the M. pusilla genome in astounding quantities, likely through a mechanism involving DNA transposition. Contrary to canonical introns, introner elements exhibit conserved sequences and lengths. Similar phenomena are known to exist in fungi. Although introner elements are known to exist in some species, no study has conducted a systematic search for them. I developed a computational pipeline for introner element detection and implemented it on all annotated assemblies on the Genbank database available through NCBI. I report putative novel IE discoveries in 38 species across 11 phyla, a major expansion upon the handful of previously known cases, which spanned only two phyla. The functional impacts of introner insertions predict evolutionary outcomes and suggest that many are deleterious while others do not display obvious functional effects. Additionally, the presence of IEs is strongly correlated with the accessibility of an organism’s germline, indicating that IEs move between species via horizontal gene transfer. My results reveal that transposons may operate as a fundamental driver of intron gain in diverse lineages.
