A novel class of Helitron- related transposable elements in maize contain portions of multiple pseudogenes Smriti Gupta 1 , Andrea Gallavotti 2 , Gabrielle A. Stryker 1 , Robert J. Schmidt 2 and Shailesh K. Lal 1, * 1 Department of Biological Sciences, Oakland University, Rochester, MI 48309-4401, USA; 2 Department of Biology, University of California, San Diego, La Jolla 92093-0116, USA (*author for correspondence: e-mail: lal@oakland.edu) Received 2 July 2004; accepted in revised form 27 November 2004 Key words: genome evolution, Helitrons, transposable elements Abstract We recently described a maize mutant caused by an insertion of a Helitron type transposable element (Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, E. and Hannah, L.C., 2003, Plant Cell, 15: 381–391). Here we describe another Helitron insertion in the barren stalk1 gene of maize. The termini of a 6525 bp insertion in the proximal promoter region of the mutant reference allele of maize barren stalk1 gene (ba1-ref) shares striking similarity to the Helitron insertion we reported in the Shrunken-2 gene. This insertion is embedded with pseudogenes that differ from the pseudogenes discovered in the mutant Shrunken-2 insertion. Using the common terminal ends of the mutant insertions as a query, we discovered other Helitron insertions in maize BAC clones. Based on the comparison of the insertion site and PCR amplified genomic sequences, these elements inserted between AT dinucleotides . These putative non-autonomous Helitron insertions completely lacked sequences similar to RPA (replication protein A) and DNA Helicases reported in other species. A blastn analysis indicated that both the 5 0 and 3 0 termini of Helitrons are repeated in the maize genome. These data provide strong evidence that Helitron type transposable elements are active and may have played an essential role in the evolution and expansion of the maize genome. Introduction Eukaryotic genomes consist largely of repetitive sequences that are derivatives of transposable elements. In humans, these elements account for up to 40% of the total genome (Lander et al., 2002). Transposable elements frequently cause mutations when they insert in genes; these muta- tions are sometimes unstable and the excision of the element can restore gene function (Feschotte et al., 2002). Until recently all known eukaryotic transposable elements, despite their diversity, could be divided into two groups based on their mode of transposition. Class 1 elements transpose via RNA intermediates catalyzed by reverse transcriptase and other proteins encoded by the element. Class 2 elements transpose via DNA intermediates catalyzed by element-encoded trans- posase (Engels, 1983; Fedoroff, 1989; Wessler, 1995). Furthermore, these transposable elements have characteristic hallmarks; their termini usually bear direct or inverted repeats and their insertion causes a characteristic and family specific 2–10 bp duplication of the target host site sequence (Doring and Starlinger, 1986; Nevers et al., 1986; Jin and Bennetzen, 1989; Singer et al., 1993; Kunze et al., 1997). There are numerous families of transposable elements that share sequence similarity and the length of their host site duplication. Within each family, transposable elements are further classified as autonomous and non-autonomous. Autono- mous elements are active members that encode all Plant Molecular Biology (2005) 57:115–127 Ó Springer 2005 DOI 10.1007/s11103-004-6636-z