Helitrons contribute to the lack of gene colinearity observed in modern maize inbreds.

U ntil recently, it was assumed that the order of gene sequences within modern maize would be virtually invariant. Recent discoveries have shown that gene colinearity is not always the case. Several laboratories (1–3) have found DNA regions rich in gene sequences that are present in some maize inbred lines but absent at homologous sites in other lines. This variation, termed ‘‘intraspecific violation of genetic colinearity’’ or ‘‘plus minus genetic polymorphism,’’ was shown by Lai et al. (4) in a recent issue of PNAS to be caused by a newly described transposable element family termed Helitrons. Lai et al. (4) revisited the 110-kb region of chromosome 9, which contains a number of genes, most notably the well characterized bronze-1 locus. Earlier work by this group (1) showed that whereas the inbred McC (for McClintock) contained sequences of 10 genes in this region, only 6 of these genes were present in this region in B73, the model inbred chosen for complete DNA sequencing. In addition, hybridization experiments showed that other lines exhibited plus minus polymorphisms for these four gene sequences that were different from McC or B73. Lai et al. (4) showed that the presence of two Helitrons in McC and their absence in B73 totally accounts for the plus minus variation of these four gene sequences. One Helitron, termed HelA, is 5.9 kb and contains three of the four polymorphic gene sequences described earlier (1). A second Helitron, HelB, is 2.7 kb and contains the fourth gene sequence distinguishing McC and B73. Sites of insertion of the two elements are separated by only 900 bp. A second, virtually identical copy of HelA was also found in the genome, albeit on a different chromosome. This second copy was also polymorphic in maize lines. Helitrons are eukaryotic transposable elements (5–8). Because Helitrons share only a few invariant sequences, they remained virtually unknown until only recently. The existence of Helitrons was first suggested (5) from computer analysis of a class of repetitive DNA in the Arabidopsis, rice, and Caenorhabditis elegans genomes. Unlike conventional transposable elements, Helitrons lack terminal repeats and do not duplicate host sequences upon insertion. The only invariant sequences are a 5 TC and a 3 CTRR. All Helitrons so far investigated have a 10to 16-bp palindrome near the 3 end and insert within a host dinucleotide, AT. Helitrons were subsequently discovered in vertebrate, white rot fungus, and mosquito genomes (6). A more concrete existence for Helitrons came from the finding that mutations at two maize genes, shrunken-2 (Sh2) (7) and