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Originally published as Genetics Published Articles Ahead of Print on April 16, 2005.

Genetics, Vol. 170, 1209-1220, July 2005, Copyright © 2005
doi:10.1534/genetics.105.040915

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DNA Rearrangement in Orthologous Orp Regions of the Maize, Rice and Sorghum Genomes

Jianxin Ma*,{dagger}, Phillip SanMiguel{ddagger}, Jinsheng Lai§, Joachim Messing§ and Jeffrey L. Bennetzen*,{dagger},1

* Department of Genetics, University of Georgia, Athens, Georgia 30602
{dagger} Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
{ddagger} Genomics Core Facility, Purdue University, West Lafayette, Indiana 47907
§ Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854

1 Corresponding author: Department of Genetics, University of Georgia, Athens, GA 30602.
E-mail: maize{at}uga.edu

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




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