Genomic diversity generated by a transposable element burst in a rice recombinant inbred population

Abstract

Genomes of all characterized higher eukaryotes harbor examples of transposable element (TE) bursts—the rapid amplification of TE copies throughout a genome. Despite their prevalence, understanding how bursts diversify genomes requires the characterization of actively transposing TEs before insertion sites and structural rearrangements have been obscured by selection acting over evolutionary time. In this study, rice recombinant inbred lines (RILs), generated by crossing a bursting accession and the reference Nipponbare accession, were exploited to characterize the spread of the very activePing/mPingfamily through a small population and the resulting impact on genome diversity. Comparative sequence analysis of 272 individuals led to the identification of over 14,000 new insertions of themPingminiature inverted-repeat transposable element (MITE), with no evidence for silencing of the transposase-encodingPingelement. In addition to new insertions,Ping-encoded transposase was found to preferentially catalyze the excision ofmPingloci tightly linked to a secondmPinginsertion. Similarly, structural variations, including deletion of rice exons or regulatory regions, were enriched for those with break points at one or both ends of linkedmPingelements. Taken together, these results indicate that structural variations are generated during a TE burst as transposase catalyzes both the high copy numbers needed to distribute linked elements throughout the genome and the DNA cuts at the TE ends known to dramatically increase the frequency of recombination.