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While studying spontaneous mutations at the maizebronze(bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate newbzmutations from severalBzstocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stablebzmutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneouswxmutations [Wessler S (1997)The Mutants of Maize, pp 385–386]. Similar mutations were recovered at the closely linkedshlocus. These events occurred with a frequency of 2–4 × 10⁻⁵in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, likeHopscotch,Magellan, andBs2, aBs1variant, were described previously; others, likeFotoandFocouin 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition ofHopscotch,Magellan, andBs2occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.

The unusual eukaryoticHelitrontransposons can readily capture host sequences and are, thus, evolutionarily important. They are presumed to amplify by rolling‐circle replication (RCR) because some elements encode predicted proteins homologous toRCRprokaryotic transposases. In support of this replication mechanism, it was recently shown that transposition of a batHelitrongenerates covalently closed circular intermediates. Another strong prediction is thatRCRshould generate tandemHelitronconcatemers, yet almost allHelitronsidentified to date occur as solo elements in the genome. To investigate alternative modes ofHelitronorganization in present‐day genomes, we have applied the novel computational tool HelitronScanner to 27 plant genomes and have uncovered numerous tandem arrays of partially decayed, truncatedHelitronsin all of them. Strikingly, most of theseHelitrontandem arrays are interspersed with other repeats in centromeres. Many of these arrays have multipleHelitron5′ ends, but a single 3′ end. The number of repeats in any one array can range from a handful to several hundreds. We propose here anRCRmodel that conforms to the presentHelitronlandscape of plant genomes. Our study provides strong evidence that plantHelitronsamplify byRCRand that the tandemly arrayed replication products accumulate mostly in centromeres.