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

Significance Rice ( Oryza sativa ) has a unique combination of attributes that made it an ideal host to track the natural behavior of very active transposable elements (TEs) over generations. In this study, we have exploited its small genome and propagation by self or sibling pollination to identify and characterize two strain pairs, EG4/HEG4 and A119/A123, undergoing bursts of the nonautonomous miniature inverted repeat transposable element mPing . Comparative sequence analyses of these strains have advanced our understanding of ( i ) factors that contribute to sustaining a TE burst for decades, ( ii ) features that distinguish a natural TE burst from bursts in cell culture or mutant backgrounds, and ( iii ) the extent to which TEs can rapidly diversify the genome of an inbred organism.