Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.

Abstract

To understand the success strategies of transposable elements (TEs) that attain high copy numbers, we analyzed two pairs of rice (<i>Oryza sativa</i>) strains, EG4/HEG4 and A119/A123, undergoing decades of rapid amplification (bursts) of the class 2 autonomous <i>Ping</i> element and the nonautonomous miniature inverted repeat transposable element (MITE) <i>mPing</i> Comparative analyses of whole-genome sequences of the two strain pairs validated that each pair has been maintained for decades as inbreds since divergence from their respective last common ancestor. Strains EG4 and HEG4 differ by fewer than 160 SNPs and a total of 264 new <i>mPing</i> insertions. Similarly, strains A119 and A123 exhibited about half as many SNPs (277) as new <i>mPing</i> insertions (518). Examination of all other potentially active TEs in these genomes revealed only a single new insertion out of ∼40,000 loci surveyed. The virtual absence of any new TE insertions in these strains outside the <i>mPing</i> bursts demonstrates that the <i>Ping/mPing</i> family gradually attains high copy numbers by maintaining activity and evading host detection for dozens of generations. Evasion is possible because host recognition of <i>mPing</i> sequences appears to have no impact on initiation or maintenance of the burst. <i>Ping</i> is actively transcribed, and both <i>Ping</i> and <i>mPing</i> can transpose despite methylation of terminal sequences. This finding suggests that an important feature of MITE success is that host recognition does not lead to the silencing of the source of transposase.