Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploidthat arose about 4.8 million years ago (Mya). As a result, maize has extensive duplicated regions within its genome.We have sequenced the two copies of one such region, generating 7.8 Mb of sequence spanning 17.4 cM of the shortarm of chromosome 1 and 6.6 Mb (25.6 cM) from the long arm of chromosome 9. Rice, which did not undergo asimilar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowedidentification of syntenic blocks, and indicated that the maize regions have undergone differential contraction ingenic and intergenic regions and expansion by the insertion of retrotransposable elements. Approximately 9% of thepredicted genes in each duplicated region are completely missing in the rice genome, and almost 20% have movedto other genomic locations. Predicted genes within these regions tend to be larger in maize than in rice, primarilybecause of the presence of predicted genes in maize with larger introns. Interestingly, the general gene methylationpatterns in the maize homoeologous regions do not appear to have changed with contraction or expansion of theirchromosomes. In addition, no differences in methylation of single genes and tandemly repeated gene copies havebeen detected. These results, therefore, provide new insights into the diploidization of polyploid species.

The homeologous Orp1 and Orp2 regions of maize and the orthologous regions in sorghum andrice were compared by generating sequence data for 486 kb of genomic DNA. At least three genicrearrangements differentiate the maize Orp1 and Orp2 segments, including an insertion of a single geneand two deletions that removed one gene each, while no genic rearrangements were detected in the maizeOrp2 region relative to sorghum. Extended comparison of the orthologous Orp regions of sorghum andjaponica rice uncovered numerous genic rearrangements and the presence of a transposon-rich region inrice. Only 11 of 27 genes (40%) are arranged in the same order and orientation between sorghum andrice. Of the 8 genes that are uniquely present in the sorghum region, 4 were found to have single-copyhomologs in both rice and Arabidopsis, but none of these genes are located near each other, indicatingfrequent gene movement. Further comparison of the Orp segments from two rice subspecies, japonica andindica, revealed that the transposon-rich region is both an ancient and current hotspot for retrotransposonaccumulation and genic rearrangement. We also identify unequal gene conversion as a mechanism formaize retrotransposon rearrangement.