Intron gains through genomic invasion of Introner-Like Elements in fungi

Introner-Like Elements (ILEs) are invasive spiceosomal introns that were identified in six fungal species, where they represent the vast majority of recent intron gains [1]. ILEs differ from Regular Spliceosomal Introns (RSIs) by their longer length and higher stability. Yet, they rapidly degenerate in length and sequence to become undistinguishable from RSIs. It was hypothesized that ILEs are the major mechanism of intron gains in fungi [2]. However, this hypothesis is not supported by their restricted taxonomic distribution. Here, we report the identification of about 10,000 typical ILEs in 53 fungal species that belong to distant classes. Intron gain analyses showed that 96% of inspected ILEs are gained introns, confirming our previous results. Remarkably, we found evidence that new ILEs can originate from other ILEs through sequence insertion, deletion and mutations. Especially in the class of Dothideomycetes, long ILEs originate from conserved short elements. Sequence analysis of these short elements revealed the presence of a motif that might be responsible for their ability to multipy because it is more conserved than splicing signals. However, while splicing signals are constrained, this conserved motif rapidly degenerates to become unidentifiable. This conserved motif could also be identified in most of long ILEs. However, in Sordariomycetes and Leotiomycetes, the motif is slightly different, which may indicate independent origins of ILEs. Altogether, our results show that ILEs are widespread in fungi and regularly emerge to give bursts of intron gains. 1. van der Burgt A, Severing E, de Wit PJ, Collemare J. 2012. Curr Biol. 22(13):1260-5. 2. Collemare J, van der Burgt A, de Wit PJ. 2013. Commun Integr Biol. 6(2):e23147.