The polychromatic Helitron landscape of the maize genome

Maize Helitron transposons are intriguing because of their notable ability to capture gene fragments and move them around the genome. To document more extensively their variability and their contribution to the remarkable genome structure variation of present-day maize, we have analyzed their composition, copy number, timing of insertion, and chromosomal distribution. First, we searched 2.4 Gb of sequences generated by the Maize Genome Sequencing Project with our HelitronFinder program. We identified 2,791 putative nonautonomous Helitrons and manually curated a subset of 272. The predicted Helitrons measure 11.9 kb on average and carry from zero to nine gene fragments, captured from 376 different genes. Although the diversity of Helitron gene fragments in maize is greater than in other species, more than one-third of annotated Helitrons carry fragments derived from just one of two genes. Most members in these two subfamilies inserted in the genome less than one million years ago. Second, we conducted a BLASTN search of the maize sequence database with queries from two previously described agenic Helitrons not detected by HelitronFinder. Two large subfamilies of Helitrons or Helitron-related transposons were identified. One subfamily, termed Cornucopious, consists of thousands of copies of an approximately 1.0-kb agenic Helitron that may be the most abundant transposon in maize. The second subfamily consists of >150 copies of a transposon-like sequence, termed Heltir, that has terminal inverted repeats resembling Helitron 3' termini. Nonautonomous Helitrons make up at least 2% of the maize genome and most of those tested show +/- polymorphisms among modern inbred lines.