Distribution, diversity, evolution, and survival of Helitrons in the maize genome.

Homology and structure-based approaches were used to identify Helitrons in the genome of maize inbred B73. A total of 1,930 intact Helitrons from eight families (62 subfamilies) and >20,000 Helitron fragments were identified, accounting for approximately 2.2% of the B73 genome. Transposition of at least one of these families is ongoing, but the most prominent burst of amplification activity was approximately 250,000 years ago. Sixty percent of maize Helitrons were found to have captured fragments of nuclear genes ( approximately 840 different fragment acquisitions, with tens of thousands of predicted gene fragments inside Helitrons within the B73 assembly). Most acquired gene fragments are undergoing random drift, but 4% were calculated to be under purifying selection, whereas another 4% exhibit apparent adaptive selection, suggesting beneficial effects for the host or Helitron transposition/retention. Gene fragment capture is frequent in some Helitron subfamilies, with as many as 10 unlinked genes providing DNA inserts within a single element. Gene fragment acquisition appears to positively influence element survival and/or ability of the Helitron to acquire additional gene fragments. Helitrons with gene fragment captures in the antisense orientation have a lesser chance of survival. Helitron distribution in maize exhibits severe biases, including preferential accumulation in relatively gene-rich regions. Insertions, however, are not usually found inside genes. Rather, Helitrons preferentially insert near (but not into) other Helitrons. This biased accumulation is not caused by a preference for cis or nearby transposition, suggesting a specific association between Helitron integration functions and unknown chromatin characteristics that specifically mark Helitrons.