Small RNA and gene silencing in Adineta vaga.
Bdelloid rotifers are freshwater invertebrates extraordinarily resistant to ionizing radiation. Such resistance can be explained as a consequence of evolutionary adaptation to survive repeated desiccation periods in their habitats that cause DNA breakage in the genome, which they are able to repair. Another unusual feature of the bdelloid rotifer Adineta vaga is transposable element (TE) content, with a high diversity of TE families, most of which appear intact, but are present at exceptionally low copy number.The goal of this project is to characterize changes in the small RNA transcriptome of A. vaga after a high dose of ionizing radiation, which introduces hundreds of DNA double-strand breaks (DSB) per genome, and see if small RNA-mediated genome defense system could be induced under these circumstances. After completion of the A. vaga genome this year, allowing us to improve TE annotation, we could map the small RNA sequencing data on the assembly and determine the regions (TEs, coding sequences, introns) that can be correlated with non-coding small RNAs. The results show that the entire TE complement (antisense reads) experiences a dramatic increase in pi-like RNA population (light green in the pie charts). Surprisingly, some of these pi-like RNAs can be mapped to the regions corresponding to single-copy insertions of TEs. Such events are found at several locations in the genome.

These results point at a genome silencing system acting against TE invasion in bdelloid rotifers, even before they have any chance to proliferate in the genome. The extraordinary resistance to ionizing radiation and desiccation, with the ability to repair the genome after extensive DNA breakage and the potential to control the TE invasion/expansion, make this organism an excellent candidate in which to study how the piRNA induction upon DNA breakage could lead to silencing of TEs, eventually followed by their elimination.