Introner Elements drive ongoing intron gain in Oikopleura dioica
Engineering
Biomolecular Engineering and Bioinformatics
Eukaryotic genes are characterized by the presence of spliceosomal introns, which interrupt genes and are removed from mRNA transcripts by a complex protein-RNA machinery called the spliceosome. Spliceosomal introns perform various functions and play a critical role in genome structure evolution, but are unequally distributed across species due to gain and loss events (Catania, F. et al 2008). Until recently, intron gain was considered to be a relatively rare event, and the fundamental drivers of intron gain are unclear. Nonetheless, transposition has long been argued to be a primary driver of intron gain based on both the possibility of a single element creating many introns and the observed concentration of intron gains in a subset of lineages, and an increasing number of studies demonstrate that several species experienced recent intron gain likely through a mechanism involving transposition (Huff et al. 2016, van der Burgt et al. 2011, Gozashti et al. in prep). A recent study from our group illustrated that transposable introns, known as introner elements (or IEs) are pervasive across diverse eukaryotic species and may act as the principal drivers for intron gain (Gozashti, L. et al. in prep). Here, we implemented molecular and computational methods to investigate how IEs can generate variation in intron positions between individuals in the same species, using the pelagic tunicate, Oikopleura dioica, as our model. We sequenced an O. dioica isolate from the San Francisco Bay and detected 27 novel candidate IEs in its genome. In addition, we found widespread variation in intron positions between Genbank’s reference isolate and our own, suggesting that intron gain is ongoing in O. dioica. We also demonstrate that IEs in O. dioica were inherited ancestrally as opposed to acquisition via horizontal gene transfer (HGT). We report evidence of heterozygous intron positions in our isolate, suggesting that introns are polymorphic within the San Francisco Bay O. dioica population. Overall, our work prefigures population genetic studies that will explore the functional impacts and fitness effects of intron gain, and provides an imperative model with which they can be conducted.
