A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5' truncations

We identified and characterized a non-long terminal repeat (LTR) retrotransposon residing primarily in subtelomeric regions of the genome in the bdelloid rotifer Adineta vaga. Contrary to the currently prevailing views on the mode of proliferation of non-LTR retrotransposons, which results in frequent formation of 5'-truncated ('dead-on-arrival') copies due to the premature disengagement of the element-encoded reverse transcriptase from its template, this non-LTR element, Hebe, is represented only by non-5'-truncated copies. Most of these copies, however, were subject to internal deletions associated with microhomologies, a hallmark of non-homologous end-joining events.The non-LTR retrotransposon Hebe from the bdelloid rotifer A. vaga was found to undergo frequent microhomology-associated deletions, rather than 5'-terminal truncations characteristic of this class of retrotransposons, and to exhibit preference for telomeric localization. These findings represent the first example of a vertically transmitted putatively deleterious TE in bdelloids, and may indicate the involvement of microhomology-mediated non-homologous end-joining in desiccation-induced double-strand break repair at the genome periphery.Mobile genetic elements are divided into two types according to their mode of transposition: retrotransposons, which require an RNA intermediate to synthesize a new copy with the aid of the element-encoded reverse transcriptase (RT), and DNA transposons, which do not require an RNA intermediate for transposition. Retrotransposons, in turn, are divided into two large classes according to the presence, or lack, of long terminal repeats (LTRs): LTR retrotransposons are framed by LTRs, while non-LTR retrotransposons are not (reviewed in [1-3]). When cDNA synthesis is primed extrachromosomally, template jumps during reverse transcription lead to the formation of LTRs. In contrast, if cDNA synthesis is primed directly at the insertion site by the 3'OH at the nick in chromos