Probing the mechanisms of intron creation in a fast-evolving mite

Abstract

Available genomic sequences from diverse eukaryotes attest to creation of millions of spliceosomal introns throughout the course of evolution, however the question of how introns are created remains unresolved. Resolution of this question has been thwarted by the fact that many modern introns appear to be hundreds of millions of years old, obscuring the mechanisms by which they were initially created. As such, analysis of lineages undergoing rapid intron creation is crucial. Recently, Hoy et al. reported the genome of the predatory mite Metaseiulus occidentalis, revealing generally rapid molecular evolution including wholesale loss of ancestral introns and gain of new ones. I sought to test several potential mechanisms of intron creation. BLAST searches did not reveal patterns of similarity between intronic sequences from different sites or between intron sequences and non-intronic sequences, which would be predicted if introns are created by propagation of pre-existing intronic sequences or by transposable element insertion. To test for evidence that introns are created by any of multiple mechanisms that are expected to lead to duplication of sequences at the two splice boundaries of an intron, I compared introns likely to have been gained in the lineage leading to M. occidentalis and likely ancestral introns. These comparisons did initially reveal greater similarity between boundaries in M. occidentalis-specific introns, however this excess appeared to be largely or completely due to greater adherence of newer introns to the so-called protosplice site, and therefore may not provide strong evidence for particular intron gain mechanisms. The failure to find evidence for particular intron creation mechanisms could reflect the relatively old age of even these introns, intron creation by variants of tested mechanisms that do not leave a clear sequence signature, or by intron creation by unimagined mechanisms.